Heyne, S., Will, S., Beckstette, M., Backofen, R. (2009) Lightweight Comparison of RNAs Based on Exact Sequence-Structure Matches 01. Bioinformatics, 25(01):2095-2102.

Beckstette, M., Mailänder, J.T., Marhöfer, R.J., Sczyrba, A., Ohlebusch, E., Giegerich, R., Selzer, P.M." (2004) Genlight: Interactive High-Throughput Sequence Analysis and comparative genomics 01. In Yearbook Bioinformatics (Hofestädt, R., ed.), Vol. 1, pp. 79-84. Köllen, Berlin, FRG.

Beckstette, M., Mailänder, J.T., Marhöfer, R.J., Sczyrba, A., Ohlebusch, E., Giegerich, R., Selzer, P.M. (2004) Genlight: Interactive High-Throughput Sequence Analysis and comparative genomics 01. Journal of Integrative Bioinformatics, 1(8):01.

Marian, C.O., Bordoli, S.J., Goltz, M., Santarella, R.A., Jackson, L.P., Danilevskaya, O., Beckstette, M., Meeley, R., Bass, H.W (2003) The Maize Single myb histone 1 gene, Smh1, belongs to a novel gene family and encodes a protein that binds telomere DNA repeats in vitro 01. Plant Physiology, 133(3):1336-1350.

Meyer, F., Kurtz, S., Backofen, R., Will, S., Beckstette, M. (2011) Structator: fast index-based search for RNA sequence-structure patterns . BMC Bioinformatics 12:214

Alawi, M., Kurtz, S., Beckstette, M. (2011) CASSys: an integrated software-system for the interactive analysis of ChIP-seq data . Journal of Integrative Bioinformatics, 8(2):155.

Heyne, S., Will, S., Beckstette, M., Backofen, R. (2008) Lightweight Comparison of RNAs Based on Exact Sequence-Structure Matches 01. International German Conference on Bioinformatics (01, ed.). Lecture Notes in Informatics.

Beckstette, M. (2007) Index-based algorithms for motif search and their integration in a system for differential genome analysis . Dissertation, Universität Bielefeld.

Martinez, P., Malde, K., Beckstette, M., Baguna, J. (2005) The origin of bilateral animals. A multigene approach 01. 01 (01, ed.). 01.

Beckstette, M., Sczyrba, A., Brivanlou, A.H., Giegerich, R., Altmann, C.R. (2005) XenDB: Full Length cDNA Prediction and Cross Species Mapping in Xenopus laevis . BMC Genomics, 6(123):01.

Sczyrba, A., Beckstette, M., Giegerich, R., Altmann, C.A. (2004) Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis 01. Proc. of German Conference on Bioinformatics (GCB) (Stoye, J., ed.). 01.

He, Y., Qin, S., Pan, X. M., Beckstette, M., Giegerich, R. (2004) Using protein secondary structure to build structural template . CASP6 method paper (01, ed.). 01.

Beckstette, M. and Sczyrba, A. and Selzer, P. M. (2004) Genlight: An Interactive System for High-throughput sequence analysis and Comparative Genomics 01. Proc. of German Conference on Bioinformatics (Stoye, J., ed.). 01.

Rarey, M., Wefing, S., Lengauer, T. (1996) Placement of medium-sized molecular fragments into active sites of proteins . Journal of Computer-Aided Molecular Design, 10:41--54.

Aberer, K., Barnickel, G., Böhm, H.J., Hemm, K., Hendlich, M., Klebe, G., Kramer, B., Lemmen, C., Lengauer, T., Mietzner, T., Rarey, M., Rippmann, F., Sander, C., Vriend, G. (1995) RELIWE: Berechnung und Vorhersage von Rezeptor-Ligand Wechselwirkungen . :27--52.

Aberer, K., Hemm, K., Kramer, B., Lemmen, C., Lengauer, T., Rarey, M. (1996) Strategische Suche nach neuen Algorithmen 01. GMD Spiegel, 1(01):01.

Rarey, M., Dixon, J.S. (1998) Feature Trees: A new molecular similarity measure based on tree matching . Journal of Computer-Aided Molecular Design, 12:471-490.

Kramer, B., Rarey, M., Lengauer, T. (1997) CASP-2 experiences with docking flexible ligands using FlexX . PROTEINS: Structure, Function and Genetics, Suppl 1:1(1):221--225.

Rarey, M., Kramer, B., Lengauer, T. (1999) The Particle Concept: Placing discrete water molecules during protein-ligand docking predictions . PROTEINS: Structure, Function and Genetics, 34(1):17--28.

Rarey, M., Kramer, B., Lengauer, T. (1999) Docking of hydrophobic ligands with interaction-based matching algorithms . Bioinformatics, 15:243--250.

Matter, H., Rarey, M. (1999) Design and Diversity Analysis of Compound Libraries for Lead Discovery . In Combinatorial Organic Chemistry (Jung, G., ed.), pp. 409--439

Kramer, B., Rarey, M., Lengauer, T. (1999) Evaluation of the FlexX incremental construction algorithm for protein-ligand docking . PROTEINS: Structure, Function and Genetics, 37:228--241.

Hoffmann, Daniel, Kramer, Bernd, Washio, Takumi, Steinmetzer, Torsten, Rarey, Matthias, Lengauer, Thomas (1999) Two-Stage Method for Protein-Ligand Docking . Journal of Medicinal Chemistry, 42:4422--4433.

Kramer, B., Metz, G., Rarey, M., Lengauer, T. (1999) Ligand Docking and Screening with FlexX 01. Medicinal Chemistry Research, 7/8(01):463--478.

Rarey, M., Lengauer, T. (2000) A Recursive Algorithm for Efficient Combinatorial Library Docking . Perspectives in Drug Discovery and Design, 20:63-81.

Rarey, M. (2001) Protein-Ligand Docking in Drug Design . In Bioinformatics (Lengauer, T., ed.), Vol. 1, pp. 315-360. Wiley-VCH.

Stahl, M., Rarey, M., Klebe, G. (2001) Screening of Drug Databases . In Bioinformatics (Lengauer, T., ed.), Vol. 2, pp. 137-170. Wiley-VCH.

Rarey, M., Kramer, B., Lemmen, C., Lengauer, T., Bernd, C., Hiller, C., Sonnenburg, F., Zimmermann, M. (1998) FlexX 1.9 User Guide 01. 01, 01(01):150.

Lemmen, C., Kramer, B., Lengauer, T., Rarey, M., Bernd, C., Hiller, C., Sonnenburg, F. (1998) FlexS 1.1 User Guide 01. 01, 01(01):01.

Rarey, M. (1997) FlexV 1.2 User Guide 01. 01, 01(01):01.

Springstubbe, S., Dröge, T., Rarey, M., Zimmer, R. (1999) Protein Strukturvorhersage und Molekulares Docking 01. Bioforum, 10(01):634--636.

Rarey, M., Stahl, M. (2001) Similarity Searching in Large Combinatorial Chemistry Spaces . Journal of Computer-Aided Molecular Design, 15:497-520.

Stahl, M., Rarey, M. (2001) A Detailed Analysis of Scoring Functions for Virtual Screening . Journal of Medicinal Chemistry, 44:1035-1042.

Rarey, M., Kramer, B., Lengauer, T. (1995) Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins . Proceedings of the Third International Conference on Intelligent Systems in Molecular Biology (Rawlings et al., C., ed.)

Muegge, I., Rarey, M. (2001) Small Molecule Docking and Scoring . In Reviews in Computational Chemistry (Lipkowitz, K.B., Boyd, D.B., ed.), Vol. 17, pp. 1-60. Wiley-VCH.

Rarey, M., Lengauer, T. (2000) Searching for New Drugs in Virtual Molecule Databases 01. (European Research Consortium for Informatics and Mathematics (ERCIM) News, 01(43):10--11.

Springstubbe, S., Rarey, M., Zimmer, R. (2000) Schneller Check beim Screening: Virtuelle Suche nach neuen Zielproteinen und Wirkstoffen in Moleküldatenbanken 01. Life Science Technologien, Supplement zu LaborPraxis, PROCESS und UmweltMagazin, Mai 2000(01):32--36.

Rarey, M., Lengauer, T. (1999) Auf's Gaspedal gedrückt: Beschleunigte Suche nach neuen Wirkstoffen in virtuellen Moleküldatenbanken 01. BioTec Das Fachmagazin für Biotechnologie, 10(5):45--46.

Rarey, M., Lengauer, T. (1999) Auf der Suche nach neuen Wirkstoffen in virtuellen Moleküldatenbanken 01. Der GMD-Spiegel, 29(3/4):20--23.

Lengauer, T., Rarey, M., Zimmer, R. (1999) Bioinformatik 01. Spektrum der Wissenschaft, Dossier Software, 01(2):38--43.

Claußen, H., Buning, C., Rarey, M., Lengauer, T. (2001) FlexE: Efficient Molecular Docking into Flexible Protein Structures . Journal of Molecular Biology, 308:377-395.

Claußen, H., Buning, C., Rarey, M., Lengauer, T. (2001) Molecular Docking into the Flexible Active Site of Aldose Reductase Using FlexE 01. Rational Approaches to Drug Design: Proceedings of the 13th European Symposium on Quantitative Structure-Activity Relationships (Höltje, H.-D., Sippl, W., ed.). Prous Science, Barcelona.

Hindle, S.A, Rarey, M., Buning, C., Lengauer, T. (2002) Flexible Docking under Pharmacophore Constraints . Journal of Computer-Aided Molecular Design, 16:129-149.

Rarey, M. (2002) Algorithmen für den computergestützten Wirkstoffentwurf 01. Habilitationsschrift.

Lengauer, T., Lemmen, C., Rarey, M., Zimmermann, M. (2004) Novel technologies for virtual screening . Drug Discovery Today, 9(1):27-34.

Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., Claussen, H., Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.-H., Gohla, R., Gossling, F., Grote, K., Heidtke, K., Herrmann, A., O\'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J. O., Lengauer, T., Liebich, I., Linden, M. van der, Luz, H., Meissner, K., Mering, C. von, Mevissen, H.-T., Mewes, H.-W., Michael, H., Mokrejs, M., Muller, T., Pospisil, H., Rarey, M., Reich, J. G., Schneider, R., Schomburg, D., Schulze-Kremer, S., Schwarzer, K., Sommer, I., Springstubbe, S., Suhai, S., Thoppae, G., Vingron, M., Warfsmann, J., Werner, T., Wetzler, D., Wingender, E., Zimmer, R. (2004) The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources . Bioinformatics, 20:268-270.

Rarey, M., Kramer, B., Bernd, C., Lengauer, T. (1996) Time-Efficient Docking of similar flexible ligands . Biocomputing: Proceedings of the 1996 Pacific Symposium (electronic version at http://www.cgl.ucsf.edu/psb/psb96/proceedings/eproceedings.html) (Hunter, L., Klein, T., ed.)

Schellhammer, I., Rarey, M. (2004) FlexX-Scan: Fast Structure-Based Virtual Screening . PROTEINS: Structure, Function, and Genetics, 57:504-517.

Zimmermann, M., Rarey, M., Naumann, T., Matter, H., Hessler, G., Lengauer, T. (2003) Extracting knowledge from high-throughput screening data: towards the generation of biophore models 01. Proceedings of the 14th EuroQSAR 2002 Symposium, Bournemouth UK: Designing Drugs and Crop Protectants: processes, problems and solutions (Ford, M., Livingstone, D., Dearden, J., Van de Waterbeemd, H., ed.). Blackwell Publishing.

Hindle, S. A., Stahl, M., Rarey, M. (2003) Flexible docking under pharmacophore type constraints: application to virtual screening 01. Proceedings of the 14th EuroQSAR 2002 Symposium, Bournemouth UK: Designing Drugs and Crop Protectants: processes, problems and solutions (Ford, M., Livingstone, D., Dearden, J., Van de Waterbeemd, H., ed.). Blackwell Publishing.

Fricker, P., Gastreich, M., Rarey, M. (2004) Automated Drawing of Structural Molecular Formulas under Constraints . Journal of Chemical Information and Computer Sciences, 44(3):1065-1078.

Gastreich, M., Lemmen, C., Briem, H., Rarey, M. (2005) Addressing the Virtual Screening Challenge - The Flex* Approach . In Virtual Screening in Drug Discovery (Alvarez, J., ed.), pp. 25-46. Decker/CRC Press.

Rarey, M., Lemmen, C., Matter, H. (2005) Algorithmic Engines in Virtual Screening . In Cheminformatics in Drug Discovery (Oprea, T. I., Kubinyi, H., Folkers, G., ed.), Vol. 23, pp. 59-115. Wiley-VCH.

Hessler, G., Zimmermann, M., Matter, H., Evers, A., Naumann, T., Lengauer, T., Rarey, M. (2005) Multiple-ligand-based virtual screening: Methods and Applications of the MTree approach . Journal of Medicinal Chemistry, 48(21):6575-6584.

Rarey, M., Maass, P., Hindle, S. A., Metz, G., Rummey, C., Zimmermann, M. (2006) Feature Trees: Theory and Applications from Large-Scale Virtual Screening to Data Analysis . In Pharmacophores and Pharmacophore Search (Langer, T., Hoffmann, R., Kubinyi, H., Folkers, G., ed.), Vol. 32, pp. 81-116. Wiley-VCH.

Rarey, M., Kramer, B., Lengauer, T., Klebe, G. (1996) A Fast Flexible Docking Method using an Incremental Construction Algorithm . Journal of Molecular Biology, 261(3):470--489.

Rarey, M., Degen, J., Reulecke, I. (2005) Docking and Scoring for Structure-Based Drug Design . In Bioinformatics - From Genomes to Therapies (Lengauer, Thomas, ed.), Vol. 2, pp. 541-600. Wiley-VCH.

Griewel, A., Rarey, M. (2005) From greedy to branch & bound and back: Assessing optimization strategies for incremental construction molecular docking tools 01. German Conference on Bioinformatics GCB 2005 (Torda, A., Kurtz, S., Rarey, M., ed.). Gesellschaft für Informatik (GI).

Rarey, M. (2005) Think Combinatorial: Computergestütztes Wirkstoffdesign mit chemischen Fragmenträumen 01. BIOforum, 01(10):56-59.

Kämper, A., Apostolakis, J., Rarey, M., Marian, C.M., Lengauer, T. (2005) Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies . Journal of Chemical Information and Modelling, 46(2):903-911.

Maaß, P., Schulz-Gasch, T., Stahl, M., Rarey, M. (2007) Recore: A fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations . Journal of Chemical Information and Modeling, 47(2):390-399.

Degen, J., Rarey, M. (2006) FlexNovo: Structure-Based Searching in Large Fragment Spaces . ChemMedChem, 1(8):854-868.

Stierand, K., Maaß, P. C., Rarey, M. (2006) Molecular Complexes at a Glance: Automated Generation of two-dimensional Complex Diagrams . Bioinformatics, 22(14):1710-1716.

Griewel, A., Rarey, M. (2006) Computational Molecular Assembly: A Geometric Hashing Approach 01. German Conference on Bioinformatics GCB 2006 (01, ed.). 01.

Schellhammer, I., Rarey, M. (2007) TrixX: Structure-Based Molecule Indexing for Large-Scale Virtual Screening in Sublinear Time . Journal of Computer-Aided Molecular Design, 21(5):223-238.

Lengauer, T., Rarey, M. (1996) Computational Methods for Biomolecular Docking . Current Opinion in Structural Biology, 6:402--406.

Reulecke, I., Lange, G., Albrecht, J., Klein, R., Rarey, M. (2008) Towards an integrated description of hydrogen bonding and dehydration: II. Reducing false positives in virtual screening using the HYDE scoring function . ChemMedChem, 3(6):885-897.

Stierand, K., Rarey, M. (2007) From Modeling to Medicinal Chemistry: Automatic generation of two-dimensional complex diagrams . ChemMedChem, 2(6):853-860.

Paern, J., Degen, J., Rarey, M. (2007) Exploring Fragment Spaces Under Multiple Physicochemical Constraints . Journal of Computer-Aided Molecular Design, 21(6):327-340.

Griewel, A., Rarey, M. (2007) Computational Reconstruction of Macromolecular Assemblies . NIC Workshop 2007 (Hansmann, U., Meinke, J., Mohanty, S., Zimmermann, O., ed.). NIC-Directors.

Seebeck, B., Reulecke, I., Kamper, A., Rarey, M. (2008) Modeling of metal interaction geometries for protein-ligand docking . Proteins, 71(3):1237-1254.

Fischer, J. R., Rarey, M. (2007) SwiFT: an index structure for reduced graph descriptors in virtual screening and clustering . Journal of Chemical Information and Modeling, 47(4):1341-53.

Degen, J., Wegscheid-Gerlach, C., Zaliani, A., Rarey, M. (2008) On the Art of Compiling and Using `Drug-Like` Chemical Fragment Spaces . ChemMedChem, 3:1503-1507.

Schlosser, J., Rarey, M. (2009) Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds . Journal of Chemical Information and Modeling, 49(4):800-809.

Lippert, T., Rarey, M. (2009) Fast automated placement of polar hydrogen atoms in protein-ligand complexes . Journal of Cheminformatics, 1(13)

Fischer, J.R., Lessel, U., Rarey, M. (2010) LoFT: Similarity-Driven Multi-Objective Focused Library Design . Journal of Chemical Information and Modeling, 50(1):1-21.

Griewel, A., Kayer, O., Schlosser, J., Rarey, M. (2009) Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size . Journal of Chemical Information and Modeling, 49(10):2303-2311.

Schmidt, L., Junker, K., Nakaigawa, N., Kinjerski, T., Weirich, G., Miller, M., Lubensky, I., Neumann, H. P., Brauch, H., Decker, J., Vocke, C., Brown, J. A., Jenkins, R., Richard, S., Bergerheim, U., Gerrard, B., Dean, M., Linehan, W. M., Zbar, B. (1999) Novel mutations of the MET proto-oncogene in papillary renal carcinomas . Oncogene, 18(14):2343-50.

Henzler, A. M., Rarey, M. (2010) In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding . Molecular Informatics, 29(3):164-173.

Henzler, A. M., Rarey, M. (2011) Protein Flexibility in Structure-Based Virtual Screening: From Models to Algorithms . In Methods and Principles in Medicinal Chemistry. Virtual Screening. Principles, Challenges, and Practical Guidelines (Sotriffer, C., ed.), pp. 223-224. Wiley-VCH Verlag GmbH & Co. KGaA.

Rarey, M., Kramer, B., Lengauer, T. (1997) Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention . Journal of Computer-Aided Molecular Design, 11:369--384.

Stierand, K., Rarey, M. (2010) Drawing the PDB - Protein-Ligand Complexes in two Dimensions . Medicinal Chemistry Letters, 1(9):540-545.

Schomburg, K., Ehrlich, H.-C., Stierand, K., Rarey, M. (2010) From Structure Diagrams to Visual Chemical Patterns . Journal of Chemical Information and Modeling, 50(9):1529-1535.

Volkamer, A., Griewel, A., Grombacher, T., Rarey, M. (2010) Analyzing the Topology of Active Sites: On the Prediction of Pockets and Sub-pockets . Journal of Chemical Information and Modeling, 50(11):2041-2052.

Ehrlich, H.-C., Rarey, M. (2011) Maximum common subgraph isomorphism algorithms and their applications in molecular science: a review . WIREs Computational Molecular Science, 1(1):68-79.

Stierand, K., Rarey, M. (2011) Flat and Easy: 2D Depiction of Protein-Ligand Complexes . Molecular Informatics, 30(1):12-19.

Huber, T., Torda, A. E. (1998) Protein Fold Recognition Without Boltzmann Statistics or Explicit Physical Basis . Protein Science, 7(1):142-149.

Dosztányi, Zs, Torda, A. E. (2001) Amino acid substitution matrices based on force fields . Bioinformatics, 17(8):686-699.

Huber, T., Torda, A. E., van Gunsteren, W. F. (1996) Optimization methods for conformational sampling using a Boltzmann-weighted mean field approach . Biopolymers, 39(1):103-114.

Procter, J, B, Perry, A.J., Torda, A.E. (2001) Comparing objects of different sizes: treating proteins as strings . Australian Journal of Chemistry, 54(6):367-374.

Torda, A. E., Scheek, R.M., van Gunsteren, W. F. (1990) Time-averaged nuclear overhauser effect distance restraints applied to tendamistat . J Mol Biol, 214(01):223-235.

Torda, A. E., van Gunsteren, W. F. (1992) Molecular modeling using nuclear magnetic resonance 01. In Reviews in computational chemistry III (Lipkowitz, KB, Boyd, DB, Boyd, DB, ed.), Vol. III, pp. 143-172. VCH.

van Gunsteren, W. F., Brunne, R. M., Gros, P., van Schaik, R. C., Schiffer, C. A., Torda, A. E. (1994) Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data 01. Methods Enzymol, 239(01):619-54..

Reith, D., Huber, T., Müller-Plathe, F., Torda, A. E. (2001) Free energy approximations in simple lattice proteins . Journal of Chemical Physics, 114(11):4998-5005.

Scott, W. R. P., Hunenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Kruger, P., van Gunsteren, W. F. (1999) The GROMOS biomolecular simulation program package . Journal of Physical Chemistry A, 103(19):3596-3607.

Russell, A, Torda, A. E. (2002) Protein sequence threading - averaging over structures . Proteins: Structure Function and Genetics, 47(01):496-505.

Huber, T., Torda, A.E. (1999) Protein sequence threading, the alignment problem and a two step strategy . Journal of Computational Chemistry, 20(14):1455-1467.

Huber, T., Torda, A. E. (2002) Protein structure prediction by threading: force field philosophy, approaches to alignment. . In Protein structure prediction: A bioinformatic approach (Tsigelny, I. F., ed.), Vol. 01, pp. 263-298. International University Line.

Torda, A. E., Procter, J. B., Huber, T. (2004) Wurst: A protein threading server with a structural scoring function, sequence profiles and optimised substitution matrices . Nucleic Acids Research, 32(01):W532-W535.

Torda, A. E. (2004) Protein sequence optimization - theory, practice and fundamental impossibility . Soft Materials, 2(01):1-10.

Kühnl, J., Bobik, T., Procter, J. B., Burmeister, C., Höppner, J., Wilde, I., Lüersen, K., Torda, A. E., Walter, R. D., Liebau, E. (2005) Functional analysis of the methylmalonyl-CoA epimerase from Caenorhabditis elegans . FEBS Journal, 272(01):1465-1477.

Vieth, S., Torda, A. E., Asper, M., Schmitz, H., Günther, S. (2004) Sequence analysis of L RNA of Lassa virus . Virology, 318(1):153-168.

Cootes, A. P., Curmi, P. M. G., Cunningham, R., Donnelly, C., Torda, A. E. (1998) The dependence of amino acid pair correlations on structural environment . Proteins-Structure Function and Bioinformatics, 32(2):175-189.

Huber, T., Torda, A. E., van Gunsteren, W. F. (1997) Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics . Journal of Physical Chemistry A, 101(33):5926-5930.

Nanzer, A. P., Torda, A. E., Bisang, C., Weber, C., Robinson, J. A., van Gunsteren, W. F. (1997) Dynamical studies of peptide motifs in the Plasmodium falciparum circumsporozoite surface protein by restrained and unrestrained MD simulations . Journal of Molecular Biology, 267(4):1012-1025.

Nanzer, A. P., Huber, T., Torda, A. E., van Gunsteren, W. F. (1996) Molecular dynamics simulation using weak-coupling NOE distance restraining . Journal of Biomolecular NMR, 8(3):285-291.

Ulrich, P., Scott, W., van Gunsteren, W.F., Torda, A. E. (1997) Protein Structure Prediction Force Fields - Parametrization With Quasi-Newtonian Dynamics . Proteins, 27(3):367-384.

Nanzer, A. P., van Gunsteren, W. F., Torda, A. E. (1995) Parametrization of Time-Averaged Distance Restraints in MD Simulations . Journal of Biomolecular NMR, 6(3):313-320.

Fennen, J., Torda, A. E., van Gunsteren, W. F. (1995) Structure Refinement with Molecular-Dynamics and a Boltmann-Weighted Ensemble . Journal of Biomolecular NMR, 6(2):163-170.

Huber, T., Torda, A. E., van Gunsteren, W. F. (1994) Local Elevation - a Method for Improving the Searching Properties of Molecular-Dynamics Simulation . Journal of Computer-Aided Molecular Design, 8(6):695-708.

Nanzer, A. P., Poulsen, F. M., van Gunsteren, W. F., Torda, A. E. (1994) A Reassessment of the Structure of Chymotrypsin Inhibitor-2 (Ci-2) Using Time-Averaged NMR Restraints . Biochemistry, 33(48):14503-14511.

Torda, A. E., van Gunsteren, W. F. (1994) Algorithms for Clustering Molecular-Dynamics Configurations . Journal of Computational Chemistry, 15(12):1331-1340.

van Gunsteren, W. F., Luque, F. J., Timms, D., Torda, A. E. (1994) Molecular Mechanics in Biology - from Structure to Function, Taking Account of Solvation . Annual Review of Biophysics and Biomolecular Structure, 23(01):847-863.

van Schaik, R. C., Berendsen, H. J. C., Torda, A. E., van Gunsteren, W. F. (1993) A Structure Refinement Method Based on Molecular-Dynamics in 4 Spatial Dimensions . Journal of Molecular Biology, 234(3):751-762.

Torda, A. E., Brunne, R. M., Huber, T., Kessler, H., van Gunsteren, W. F. (1993) Structure Refinement Using Time-Averaged J-Coupling Constant Restraints . Journal of Biomolecular NMR, 3(1):55-66.

van Gunsteren, W. F., Gros, P., Torda, A. E., Berendsen, H. J. C., van Schaik, R. C. (1991) On Deriving Spatial Protein-Structure from NMR or X-Ray-Diffraction Data ://A1991GP94800010. Ciba Foundation Symposia, 161(01):150-166.

Torda, A. E., van Gunsteren, W. F. (1991) The Refinement of NMR Structures by Molecular-Dynamics Simulation . Computer Physics Communications, 62(2-3):289-296.

Torda, A. E. (1997) Perspectives in protein-fold recognition . Curr Opin Struct Biol, 7(2):200-5.

Torda, A. E., Scheek, R. M., van Gunsteren, W. F. (1989) Time-Dependent Distance Restraints in Molecular-Dynamics Simulations . Chemical Physics Letters, 157(4):289-294.

Torda, A. E., Norton, R. S. (1989) Proton NMR Relaxation Study of the Dynamics of Anthopleurin-a in Solution . Biopolymers, 28(3):703-716.

Torda, A. E., Mabbutt, B. C., van Gunsteren, W. F., Norton, R. S. (1988) Backbone Folding of the Polypeptide Cardiac Stimulant Anthopleurin-a Determined by Nuclear Magnetic-Resonance, Distance Geometry and Molecular-Dynamics . Febs Letters, 239(2):266-270.

Torda, A. E., Norton, R. S. (1987) Amide Proton-Exchange Rates in Cardioactive Sea-Anemone Polypeptides ://A1987K456200020. Biochemistry International, 15(3):659-666.

Torda, A. E., Baldwin, G. S., Norton, R. S. (1984) High-Resolution H1NMR Studies of Human Gastrin 01. Proceedings of the Australian Biochemical Society, 16(01):18-18.

Torda, A. E., Baldwin, G. S., Norton, R. S. (1985) High-Resolution Proton Nuclear Magnetic-Resonance Studies of Human Gastrin . Biochemistry, 24(7):1720-1727.

Nguyen, P.H., Mittag, E., Torda, A.E., Stock, G. (2006) Improved Wang-Landau sampling through the use of a generalised effective potential . Journal of Chemical Physics, 124(01):154107.

Jordanova, R., Radoslavov, G., Fischer, P., Torda, A. E., Lottspeich, F., Boteva, R., Walter, R. D., Bankov, I., Liebau, E. (2005) The highly abundant protein Ag-Ibp55 from Ascaridia galli represents a novel type of lipid-binding proteins . Journal of Biological Chemistry, 280(50):41429-41438.

Schenk, G., Margraf, Th., Torda, A. (2008) Protein sequence and structure alignments within one framework . Algorithms for Molecular Biology, 3(4):10.1186/1748-7188-3-4.

Margraf, Th., Schenk, G., Torda, A. E. (2009) The SALAMI protein structure search server . Nucleic Acids Research, 37(suppl 2):W480-W484.

Kleesiek, J., Torda, A.E. (2009) RNA secondary structure prediction using a self-consistent mean field approach . Journal of Computational Chemistry, 31(6):1135-1142.

Kong, S-G., Fan, W-L., Chen, H-D., Wigger, J., Torda, A.E., Lee, H.C. (2009) A quantitative measure of randomness and order for complete genomes 01. Physical Reviews, 01(01):01.

Torda, A.E. (2005) Protein Threading 01. In The Proteomics Handbook (Walker, J.M., ed.), Vol. 01, pp. 921-938. Humana Press.

Nield, B.S., Willows, R.D., Torda, A.E., Gillings, M.R., Holmes, A.J., Nevalainen, K.M.H., Stokes, H.W., Mabbutt, B.M. (2004) New enzymes from environmental cassette arrays: Functional attributes of a phosphotransferase and a RNA-methyltransferase 01. Protein Sciences, 13(01):1651-1659.

Cootes, A.P., Curmi, P.M.G., Torda, A.E. (2000) Automated Protein Design and Sequence Optimisation: Scoring Functions and the Search Problem 01. Current Protein & Peptide Science, 3(01):255-271.

Torda, A.E. (1997) Guessing protein structures 01. Trends in Biotechnology, 15(01):380-381.

van Gunsteren, W.F., Nanzer, A.P., Torda, A.E. (1996) Molecular simulation methods for generating ensembles or trajectories consistent with experimental data 01. Monte Carlo and Molecular Dynamics of Condensed Matter (Binder, K., Cicotti, G., ed.). Ital. Phys. Soc. Bologna.

van Gunsteren, W.F., Huber, T., Torda, A.E. (1995) Biomolecular modelling: overview of methodsto search and sample conformational space 01. European Conference on Computational Chemistry (Bernardi, F., Rivali, J-L., ed.). 01.

Scheek, R.M., Torda, A.E., Kemminck, J., van Gunsteren, W.F. (1991) Structure Determination by NMR: The Modeling of NMR Parameters as Ensemble Averages 01. In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (Hoch, J.C., Poulsen, F.M., Redfield, C., ed.), Vol. 01, pp. 209-218. 01.

Ayers, D.J., Gooley, P.R., Widmer-Cooper, A., Torda, A.E. (1999) Enhanced protein fold recognition using secondary structure information from NMR . Protein Science, 8(01):1127-1133.

Torda, A.E., Scheek, R.M., van Gunsteren, W.F. (1991) Time Average Distance Restraints in NMR Based Structural Refinement 01. In Computational Aspects of the Study of Biological Macrmolecules by Nuclear Magnetic Resonance Spectroscopy (Hoch, J.C., Poulsen, F.M., Redfield, C., ed.), Vol. 01, pp. 219-226. 01.

Textor, J., Hansen, B. (2009) Hybrid Simulation Algorithms for an Agent-Based Model of the Immune Response 01. Cybernetics and Systems, 40(5):390-417.

Huber, T., Russell, A.J., Ayers, D., Torda, A.E. (1999) SAUSAGE: Protein threading with flexible force fields . Bioinformatics, 15(01):1064-1065.

Ayers, D. J., Huber, T., Torda, A. E. (1999) Protein fold recognition score functions: unusual construction strategies . Proteins, 36(4):454-461.

Cootes, A. P., Curmi, P. M. G., Torda, A. E. (2000) Biased Monte Carlo optimization of protein sequences . Journal of Chemical Physics, 113(6):2489-2496.

Abouelhoda, M. I., Kurtz, S., Ohlebusch, E. (2006) Enhanced suffix arrays and applications . In Handbook on Computational Molecular Biology (Aluru, S., ed.), Vol. 01, pp. 7-1--7-27. Chapman and Hall/CRC.

Hoffmann, S., Otto, C., Kurtz, S., Sharma, C. M., Khaitovich, P., Vogel, J., Stadler, P. F., Hackermueller, J. (2009) Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures . PLoS Comput Biol, 5(9):e1000502.

Beckstette, M., Homann, R., Giegerich, R., Kurtz, S. (2009) Significant speedup of database searches with HMMs by search space reduction with PSSM family models . Bioinformatics, 25:3251-3258.

Schmitz-Huebsch, D.J., Kurtz, S. (2010) MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects 01. In Metagenomics. Methods in Molecular Biology (Daniel, R., Streit, W., ed.), Vol. 668, pp. 325-338. Springer.

Agelopoulos, K., Greve, B., Schmidt, H., Pospisil, H., Kurtz, S., Bartkowiak, K., Andreas, A., Wieczorek, M., Korsching, E., Buerger, H., Brandt, B. H. (2010) Selective regain of egfr gene copies in CD44+/CD24-/low breast cancer cellular model MDA-MB-468 . BMC Cancer, 10(1):78.

Farnbacher, M., Jahns, T., Willrodt, D., Daniel, R., Haas, R., Goesmann, A., Kurtz, S., Rieder, G. (2010) Sequencing, annotation and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8 . BMC Genomics, 11(1):335.

Alawi, M., Kurtz, S., Beckstette, M. (2011) CASSys: an integrated software system for the interactive analysis of ChIP-seq data . International Symposium on Integrative Bioinformatics (IB2011)

Mader, M., Simon, R., Steinbiss, S., Kurtz, S. (2011) FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context . Journal of Clinical Bioinformatics, 1:20.

Brendel, V., Kurtz, S., Walbot, V. (2002) Comparative genomics of Arabidopsis and Maize: Prospects and limitations . Genome Biology, 3(3):reviews1005.1--1005.6.

Brett, D., Pospisil, H., Valcarcel, J., Reich, J., Bork, P. (2002) Alternative splicing and genome complexity . Nature Genetics, 30(1):29--30.

Campos-Gongora, E., Ebert, F., Willhoeft, U., Said-Fernandez, S., Tannich, E. (2004) Characterization of chitin synthases from Entamoeba . Protist, 155(01):323--330.

Chain, P., Kurtz, S., Ohlebusch, E., Slezak, T. R. (2003) An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges . Briefings in Bioinformatics, 4(2):105--123.

Choudhuri, J. V., Schleiermacher, C., Kurtz, S., Giegerich, R. (2004) Genalyzer: Interactive visualization of sequence similarities between entire genomes . Bioinformatics, 20(01):1964--1965.

Dong, Q., Lawrence, C. J., Schlueter, S. D., Wilkerson, M. D., Kurtz, S., Lushbough, C., Brendel, V. (2005) Comparative plant genomics resources at PlantGDB . Plant Physiology, 139(2):610--618.

Fitch, J. P., Gardner, S. N., Kuczmarski, T. A., Kurtz, S., Myers, R., Ott, L. L., Slezak, T. R., Vitalis, E. A., Zemla, A. T., McCready, P. M. (2002) Rapid development of nucleic acid diagnostics . Proceedings of the IEEE, 90(11):1708--1721.

Futamura, N., Aluru, S., Kurtz, S. (2001) Parallel suffix sorting . Proceedings of the Ninth International Conference on Advanced Computing and Communications, Bhubaneshwar, India (Iyengarm, S.S., Sinha, B. P., ed.). Tata McGraw-Hill.

Abouelhoda, M. I., Kurtz, S., Ohlebusch, E. (2004) Replacing suffix trees with enhanced suffix arrays . Journal of Discrete Algorithms, 2(01):53--86.

Giegerich, R., Hinze, R., Kurtz, S. (1999) Straight to the heart of computer science via functional programming . Proceedings of the Workshop on Functional and Declarative Programming in Education (01, ed.). Technical Report Rice COMP TR99-346, Department of Computer Science, Rice University, Editor: Matthias Felleisen.

Giegerich, R., Hischke, F., Kurtz, S., Ohlebusch, E. (1997) A general technique to improve filter algorithms for approximate string matching . Proceedings of Fourth South American Workshop on String Processing, Valparaiso, Chile (01, ed.). Carleton University Press.

Giegerich, R., Kurtz, S. (1997) From Ukkonen to McCreight and Weiner: A unifying view of linear-time suffix tree construction . Algorithmica, 19(01):331--353.

Giegerich, R., Kurtz, S. (1995) A comparison of imperative and purely functional suffix tree constructions . Science of Computer Programming, 25(2-3):187--218.

Giegerich, R., Kurtz, S., Stoye, J. (2003) Efficient implementation of lazy suffix trees . Software---Practice and Experience, 33(11):1035--1049.

Giegerich, R., Kurtz, S., Stoye, J. (1999) Efficient implementation of lazy suffix trees . Proceedings of the Third Workshop on Algorithmic Engineering (WAE99) (01, ed.). Lecture Notes in Computer Science 1668.

Giegerich, R., Kurtz, S., Weiller, G. F. (1999) An algebraic dynamic programming approach to the analysis of recombinant DNA sequences . Proceedings of Workshop on Algorithmic Ascpects of Advanced Programming Languages (WAAAPL), Paris, September 1999 (01, ed.). 01.

Gremme, G., Brendel, V., Sparks, M. E., Kurtz, S. (2005) Engineering a software tool for gene prediction in higher organisms . Information and Software Technology, 47(15):965--978.

Gräf, S., Nielsen, F. G. G., Kurtz, S., Huynen, M. A., Birney, E., Stunnenberg, H., Flicek, P. (2007) Optimized design and assessment of whole genome tiling arrays . Bioinformatics, 23 ISMB/ECCB 2007(01):i195--i204.

Gräf, S., Strothmann, D., Kurtz, S., Steger, G. (2001) HyPaLib: A database of RNAs and RNA structural elements defined by hybrid patterns . Nucleic Acids Res., 29(1):196--198.

Abouelhoda, M. I., Kurtz, S., Ohlebusch, E. (2002) The enhanced suffix array and its applications to genome analysis . Proceedings of the Second Workshop on Algorithms in Bioinformatics (01, ed.). Lecture Notes in Computer Science 2452, Springer-Verlag.

Gräf, S., Teune, J. H., Strothmann, D., Kurtz, S., Steger, G. (2006) A computational approach to search for non-coding RNAs in genomic data 01. In Small RNAs: Analysis and Regulatory Functions. (Nellen, W., Hammann, C., ed.), Vol. 17, pp. 57--74. Springer Verlag.

Hanauske, A. R., Eismann, U., Oberschmidt, O., Pospisil, H., Hoffmann, S., Hanauske-Abel, H., Ma, D., Chen, V., Paoletti, P., Niyikiza, C. (2007) In vitro chemosensitivity of freshly explanted tumor cells to pemetrexed is correlated with target gene expression . Investigational New Drugs, 25(5):417-23.

Hegasy, G. A., Willhoeft, U., Majno, S. A., Seeberger, H., Zipfel, P. F., Hellwage, J. (2003) Pig complement regulator factor H: Molecular cloning and functional characterization . Immunogenetics, 55(01):462--471.

Höchsmann, M., Töller, T., Giegerich, R., Kurtz, S. (2003) Local similarity in RNA secondary structures . Proc of the Computational Systems Bioinformatics Conference, Stanford, CA, August 2003 (CSB 2003) (01, ed.). 01.

Höhl, M., Kurtz, S., Ohlebusch, E. (2002) Efficient multiple genome alignment . Bioinformatics, 18(Suppl. 1):S312--S320.

Krüger, J., Sczyrba, A., Kurtz, S., Giegerich, R. (2004) e2g: An interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences . Nucleic Acids Res., 32(01):W301--W304.

Kurtz, S. (1999) Reducing the space requirement of suffix trees . Software---Practice and Experience, 29(13):1149--1171.

Kurtz, S. (1996) Approximate string searching under weighted edit distance . Proceedings of Third South American Workshop on String Processing, Recife, Brazil (01, ed.). Carleton University Press.

Kurtz, S., Balkenhol, B. (2000) Space efficient linear time computation of the Burrows and Wheeler transformation . In Numbers, Information and Complexity (Althöfer, I., Cai, N., Dueck, G., Khachatrian, L., Pinsker, M. S., Sarközy, A., Wegener, I., Zhang, Z., ed.), Vol. 01, pp. 375--383. Kluwer Academic Publishers.

Kurtz, S., Choudhuri, J. V., Ohlebusch, E., Schleiermacher, C., Stoye, J., Giegerich, R. (2001) REPuter: The manifold applications of repeat analysis on a genomic scale . Nucleic Acids Res., 29(22):4633--4642.

Abouelhoda, M. I., Ohlebusch, E., Kurtz, S. (2002) Optimal exact string matching based on suffix arrays . Proceedings of the Ninth International Symposium on String Processing and Information Retrieval (01, ed.). Lecture Notes in Computer Science 2476, Springer-Verlag.

Kurtz, S., Lonardi, S. (2004) Computational Biology 01. In Handbook on Data Structures and Applications (Mehta, D. P., Sahni, S., ed.), Vol. 01, pp. 58-1 -- 58-17. Chapman and Hall/CRC.

Kurtz, S., Myers, G. (1997) Estimating the probability of approximate matches . Proceedings of the Annual Symposium on Combinatorial Pattern Matching (CPM'97), Lecture Notes in Computer Science 1075 (01, ed.). Springer Verlag.

Kurtz, S., Ohlebusch, E., Schleiermacher, C., Stoye, J., Giegerich, R. (2000) Computation and visualization of degenerate repeats in complete genomes . Proceedings of the International Conference on Intelligent Systems for Molecular Biology (01, ed.). AAAI Press.

Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., Salzberg, S. L. (2004) Versatile and open software for comparing large genomes . Genome Biology, 5(R12):01.

Kurtz, S., Schleiermacher, C. (1999) REPuter: Fast computation of maximal repeats in complete genomes . Bioinformatics, 15(5):426--427.

Loftus, B., Anderson, I., Davies, R., Alsmark, U. C., Samuelson, J., Amedeo, P., Roncaglia, P., Berriman, M., Hirt, R. P., J, B., Nozaki, T., Suh, B., Pop, M., Duchene, M., Ackers, J., Tannich, E., Leippe, M., Hofer, M., Bruchhaus, I., Willhoeft, U., Bhattacharya, A., Chillingworth, T., Churcher, C., Hance, Z., Harris, B., Harris, D., Jagels, K., Moule, S., Mungall, K., Ormond, D., Squares, R., Whitehead, S., A, M., Rabbinowitsch, E., Norbertczak, H., Price, C., Wang, Z., Guillen, N., Gilchrist, C., Stroup, S. E., Bhattacharya, S., Lohia, A., Foster, P. G., Sicheritz-Ponten, T., Weber, C., Singh, U., Mukherjee, C., El-Sayed, N. M., Petri, W. A., Jr., Clark, C. G., Embley, T. M., Barrell, B., Fraser, C. M., Hall, N. (2005) The Genome of the protist parasite Entamoeba histolytica . Nature, 433(01):865--868.

Meyer, S., Pospisil, H., Scholten, S. (2007) Heterosis associated gene expression in maize embryos 6 days after fertilization exhibits additive, dominant and overdominant pattern . Plant Mol Biol, 63(3):381--391.

Pobigaylo, N., Wetter, D., Szymczak, S., Schiller, U., Kurtz, S., Meyer, F., Nattkemper, T. W., Becker, A. (2006) Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti . Appl Environ Microbiol., 72(6):4329--4337.

Pospisil, H. (2006) Identification of embryo specific human isoforms using a database of predicted alternative splice forms . Journal of Integrative Bioinformatics, 17(01):01.

Pospisil, H., Herrmann, A., Bortfeldt, R. H., Reich, J. (2004) EASED: Extended alternatively spliced EST database . Nucleic Acid Res., 32(1):Database Issue 70--74.

Balkenhol, B., Kurtz, S. (2000) Universal data compression based on the Burrows and Wheeler transformation: Theory and practice . IEEE Trans. on Computers, 49(1):1043--1053.

Pospisil, H., Herrmann, A., Butherus, K., Pirson, S., Reich, J. G., Kemmner, W. (2006) Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5) and the altered Axin-1 expression euring tumour progression . BMC Genomics, 7(01):148.

Pospisil, H., Herrmann, A., Pankow, H., Reich, J. (2003) A database on alternative splice forms on the Integrated Genetic Map Service (IGMS) . In Silico Biology, 3(01):229--234.

Pospisil, H., Holzhütter, H. G. (2001) A compartment model to calculate time-dependent concentration profiles of topically applied chemical compounds in the anterior compartments of the rabbit eye . ATLA, 29(3):347--365.

Reich, J., Pospisil, H. (2003) Splice variants of gene expression---a source for diversity of the human proteome . Proceedings of the XIIth International Congress on Genes, Gene Families and Isozymes (01, ed.). Moduzzi Editore International Proceedings Division.

Sarkar, A., Coates, C. J., Whyard, S., Willhoeft, U. Atkinson P. W., O'Brochta, D. A. (1997) The Hermes element from Musca domestica can transpose in four families of cyclorrhaphan flies . Genetica, 99(01):15-29.

Sczyrba, A., Krüger, J., Mersch, H., Kurtz, S., Giegerich, R. (2003) RNA-related tools on the Bielefeld Bioinformatics Server . Nucleic Acids Res., 31(13):3767--3770.

Traut, W., Willhoeft, U. (1990) A jumping sex determining factor in the fly Megaselia scalaris 01. Chromosoma, 99(01):407--412.

Willhoeft, U. (1997) Fluorescence in situ hybridization of ribosomal DNA to mitotic chromosomes of tsetse flies (Diptera: Glossinidae: Glossina) . Chromosome Res., 5(01):262--267.

Willhoeft, U., Buss, H., Tannich, E. (2000) Genetic differences between Entamoeba histolytica and Entamoeba dispar . Arch. Med. Res., 31(01):S254.

Willhoeft, U., Buß, H., Tannich, E. (2002) The abundant polyadenylated transcript 2 DNA sequence of the pathogenic protozoan parasite Entamoeba histolytica represents a nonautonomous non-long-terminal-repeat retrotransposon-like element which is absent in the closely related nonpathogenic species Entamoeba dispar . Infect. Immun., 70(01):6798--6804.

Balkenhol, B., Kurtz, S., Shtarkov, Y. M. (1999) Modification of the Burrows and Wheeler data compression algorithm . Proceedings of the IEEE Data Compression Conference, Snowbird, Utah (01, ed.). IEEE Computer Society Press.

Willhoeft, U., Buß, H., Tannich, E. (1999) Analysis of cDNA expressed sequence tags from Entamoeba histolytica: Identification of two highly abundant polyadenylated transcripts with no overt open reading frames . Protist, 150(01):61--70.

Willhoeft, U., Buß, H., Tannich, E. (1999) DNA sequences corresponding to the ariel gene family of Entamoeba histolytica are not present in E. dispar . Parasitol. Res., 85(01):787--789.

Willhoeft, U., Campos-Congares, E., Touzni, S., Bruchhaus, I., Tannich, E. (2001) Introns of Entamoeba histolytica and Entamoeba dispar . Protist, 152(01):149--156.

Willhoeft, U., Franz, G. (1996) Identification of the sex determining region of the Ceratitis capitata Y chromosome by deletion mapping . Genetics, 144(01):739--745.

Willhoeft, U., Franz, G. (1996) Comparison of the mitotic karyotypes of Ceratitis capitata, Ceratitis rosa and Trirhithrum coffeae (Diptera: Tephritidae) by C-banding and FISH 01. Genome, 39(01):884--889.

Willhoeft, U., Franz, G., McInnis, D. (1996) Towards the application of genetic sexing in tephritid fruit fly SIT programs 01. Fruit Flies Pests: A World Assessment of their Biology and Management, Proceedings of the 4th Int. Symp. on Fruit Flies of Economic Importance (McPheron, B. A., Steck, G. J., ed.). St. Lucie Press, Delray Beach, Florida.

Willhoeft, U., Hamann, L., Tannich, E. (1999) A DNA sequence corresponding to the gene encoding cysteine proteinase 5 in Entamoeba histolytica is present and positionally conserved but highly degenerated in Entamoeba dispar . Infect. Immun., 67(01):5925--5929.

Willhoeft, U., Mueller-Navia, J., Franz, G. (1998) Analysis of the sex chromosomes of the Mediterranean fruit fly by microdissected DNA probes 01. Genome, 41(01):74--78.

Willhoeft, U., Tannich, E. (2000) Fluorescence microscopy and fluorescence in situ hybridization of Entamoeba histolytica nuclei to analyse mitosis and localization of repetitive DNA . Mol. Biochem. Parasitol., 105(01):291--296.

Willhoeft, U., Tannich, E. (1999) The electrophoretic karyotype of Entamoeba histolytica . Mol. Biochem. Parasitol., 99(01):41--53.

Beckstette, M., Homann, R., Giegerich, R., Kurtz, S. (2006) Fast index based algorithms and software for matching position specific scoring matrices . BMC Bioinformatics, 7(01):389.

Willhoeft, U., Traut, W. (1995) The sex-determining region of the Megaselia scalaris (Diptera) Y chromosome . Chromosome Res., 3(01):59--65.

Willhoeft, U., Traut, W. (1990) Molecular differentiation of the homomorphic sex chromosomes in Megaselia scalaris (Diptera) detected by random DNA probes . Chromosoma, 99(01):237--242.

Zingler, N., Willhoeft, U., Brose, H. P., Schoder, V., Jahns, T., Hanschmann, K. M. O., Morrish, T. A., Löwer, J., Schumann, G. (2005) Analysis of 5' junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5' end attachment requiring microhomology-mediated end joining . Genome Research, 15(01):780--789.

Hanauske, A. R., Eismann, U., Oberschmidt, O., Pospisil, H., Hanauske-Abel, H. M., Blatter, J., Ma, D., Chen, V., Lahn, M. (2007) Correlations of mRNA expression and in vitro chemosensitivity to enzastaurin in freshly explanted human tumor cells . Invest New Drugs, 26(3):215-22.

Brendel, V., Kurtz, S., Pan, X. (2007) Visualization of syntenic relationships with SynBrowse . In Comparative Genomics (Bergmann, N.H., ed.), Vol. 2, pp. 153-164. Humana Press.

Ellinghaus, D., Kurtz, S., Willhoeft, U. (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons . BMC Bioinformatics, 9(1):18.

Ohlebusch, E., Kurtz, S. (2008) Space efficient computation of rare maximal exact matches between multiple sequences . Journal of Computational Biology, 15(4):357-377.

Herold, J., Kurtz, S., Giegerich, R. (2008) Efficient computation of absent words in genomic sequences . BMC Bioinformatics, 9:167.

Scheja, L., Heese, B., Zitzer, H., Michael, M.D., Siesky, A.M., Pospisil, H., Beisiegel, U., Seedorf, K. (2008) Acute-Phase Serum Amyloid A as a Marker of Insulin Resistance in Mice . Experimental Diabetes Research, Volume 2008, Article ID 230837(01):1--11.

Helms, M., Kemming, D., Pospisil, H., Vogt, U., Buerger, H., Korsching, E., Liedtke, C., Schlotter, C.M., Brandt, H.B. (2008) Squalene epoxidase, located at chromosome 8q24.1, is upregulated in 8q+ breast cancer and indicates poor clinical
outcome in stage I and II disease . British Journal of Cancer, 99(01):774--780.

Beckstette, M., Strothmann, D., Homann, R., Giegerich, R., Kurtz, S. (2004) PoSSuMsearch: Fast and sensitive matching of position specific scoring matrices using enhanced suffix arrays . Proc. of the German Conference on Bioinformatics (Giegerich, R., Stoye, J., ed.)

Scheja, L., Toedter, K., Mohr, R., Niederfellner, G., Michael, M.D., Meissner, A., Schoettler, A., Pospisil, H., Beisiegel, U., Heeren, J. (2008) Liver TAG Transiently decreases While PL n-3 and n-6 Fatty Acids are Persistently Elevated in Insulin Resistant Mice . Lipids, 43(01):1039 -1051.

Kurtz, S., Narechania, A., Stein, J.C., Ware, D. (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes . BMC Genomics, 9:517.

Abouelhoda, M.I., Kurtz, S., Ohlebusch, E. (2008) CoCoNUT: an efficient system for the comparison and analysis of genomes . BMC Bioinformatics, 9:476.

Steinbiss, S., Gremme, G., Schaerfer, C., Mader, M., Kurtz, S. (2009) AnnotationSketch: a genome annotation drawing library . Bioinformatics, 25(4):533-534.

Koscielny, G., Texier, V. Le, Gopalakrishnan, C., Kumanduri, V., Riethoven, J.-J., Nardone, F., Stanley, E., Fallsehr, C., Hofmann, O., Kull, M., Harrington, E., Boué, S., Eyras, E., Plass, M., Lopez, F., Ritchie, W., Moucadel, V., Ara, T., Pospisil, H., Herrmann, A., Reich, J. G., Guigó, R., Bork, P., Knebel Doeberitz, M. von, Vilo, J., Hide, W., Apweiler, R., Thanaraj, T. A., Gautheret, D. (2009) ASTD: The Alternative Splicing and Transcript Diversity Database . Genomics, 93(3):213-220.

Bortfeld, R., Herrmann, A., Pospisil, H., Schuster, S. (2007) Validation of human alternative splice forms using the EASED platform and multiple splice site discriminating features . In Mathematical Modeling of Biological Systems, Volume I Cellular Biophysics, Regulatory Networks, Development, Biomedicine, and Data Analysis (Series: Modeling and Simulation in Science, Engineering and Technology) (Deutsch, A., Brusch, L., Byrne, H., de Vries, G., Herzel, H., ed.)

Helms, M. W., Kemming, D., Contag, C. H., Pospisil, H., Bartkowiak, K., Wang, A., Chang, S.-Y., Buerger, H., Brandt, B. H. (2009) TOB1 Is Regulated by EGF-Dependent HER2 and EGFR Signaling, Is Highly Phosphorylated, and Indicates Poor Prognosis in Node-Negative Breast Cancer . Cancer Res, 69(12):5049--5056.

Dancau, A.-M., Wuth, L., Waschow, M., Holst, F., Krohn, A., Choschzick, M., Terracciano, L., Politis, S., Kurtz, S., Lebeau, A., Friedrichs, K., Wencke, K., Monni, O., Simon, R. (2010) PPFIAI and CCNDI are Frequently Coamplified in Breast Cancer . Genes, Chromosomes & Cancer, 49(1):1--8.

Steinbiss, S., Willhoeft, U., Gremme, G., Kurtz, S. (2009) Fine-grained annotation and classification of de novo predicted LTR retrotransposons . Nucleic Acids Research, 37(21):7002 - 7013.

Beuck, S., Schwabe, T., Grimme, S., Schlörer, N., Schänzer, W., Thevis, M. (2009) Unsusal Mass Spectrometric Dissociation Pathway of Protonated Isoquinoline-3-carboxamides due to Multiple Reversible Water Addition in the Gas Phase . J. Am. Soc. Mass Spec., 20:2034-2048.

Grimme, S., Antony, J., Schwabe, T., Mück-Lichtenfeld, C. (2007) Density Functional Theory With Dispersion Corrections For Supramolecular Structures, Aggregates, And Complexes Of (Bio)Organic Molecules . Org. Biomol. Chem., 5:741-758.

Neese, F., Schwabe, T., Grimme, S. (2007) Analytic Derivatives For Perturbatively Corrected Double Hybrid Density Functionals: Theory, Implementation, And Applications . J. Chem. Phys., 126:124115-15.

Neese, F., Schwabe, T., Kossmann, S., Schirmer, B., Grimme, S. (2009) Assessment of Orbital Optimized, Spin Component Scaled Second Order Many Body Perturbation Theory for Thermochemistry and Kinetics . J. Chem. Theory Comput., 5:3060-3073.

Schwabe, T., Grimme, S. (2006) Towards Chemical Accuracy For The Thermodynamics Of Large Molecules: New Hybrid Density Functionals Including Non-local Correlation Effects . Phys. Chem. Chem. Phys., 8:4398-4401.

Schwabe, T., Grimme, S. (2007) Double-hybrid Density Functionals With Long-range Dispersion Corrections: Higher Accuracy And Extended Applicability . Phys. Chem. Chem. Phys., 9:3397-3406.

Schwabe, T., Grimme, S. (2008) Theoretical Description Of Substituent Effects In Electrophilic Aromatic Substitution Reactions . Eur. J. Org. Chem., 2008:5928-5935.

Schwabe, T., Grimme, S. (2008) Theoretical Thermodynamics For Large Molecules: Walking The Thin Line Between Accuracy And Computational Cost . Acc. Chem. Res., 41:569-579.

Schwabe, T., Grimme, S. (2009) The Benzenium-Ethene Complex: A Fundamental Problem For Standard Second-Order Möller-Plesset . Theory, J. Phys. Chem. A, 113:3005-3008.

Schwabe, T., Grimme, S. (2010) Calculation of Magnetic Couplings with Double-Hybrid Density Functionals . J. Phys. Chem. Lett., 1:1201-1204.

Schwabe, T., Grimme, S., Djukic, J.-P. (2009) Non-Covalent Metal-Metal Interactions: the Crucial Role of London-Dispersion in a Bimetallic Indenyl System . J. Am. Chem. Soc., 131:14156-14157.

Schwabe, T., Haugaard Olsen, J.M., Sneskov, K., Kongsted, J., Christiansen, O. (2011) Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable
Embedding Calculations . J. Chem. Theory Comput., 7:2209-2217.

Schwabe, T., Huenerbein, R., Grimme, S. (2010) Large Molecules - Small Energies: Challenges for Contemporary Quantum Chemistry . Synlett, 10:1431-1441.

Sneskov, K., Schwabe, T., Christiansen, O., Kongsted, J. (2011) Scrutinizing the effects of polarization in QM/MM excited state calculations . Phys. Chem. Chem. Phys., 13:18551-18560.

Sneskov, K., Schwabe, T., Kongsted, J., Christiansen, O. (2011) The Polarizable Embedding Coupled Cluster Method . J. Chem. Phys., 134:104108.

Stierand, K., Rarey, M. (2011) Consistent two-dimensional visualization of protein-ligand complex series . Journal of Cheminformatics, 3(21):Online-Publication.

Seebeck, B., Wagener, M., Rarey, M. (2011) From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses . ChemMedChem, 6(9):1630-1639.

Lemcke, T., Dreher, J., Rarey, M., Totzke, F., Schächtele, C., Kubbutat, M. H. G., Kunick, C. (2011) Identification of Inhibitors of the Tyrosine Kinase c-Met by
Structure-Based Virtual Screening . Molecular Informatics, 30(2-3):145-150.

Fischer, J. R., Lessel, U., Rarey, M. (2011) Improving Similarity-Driven Library Design: Customized Matching an Regio-Selective Feature Trees . Journal of Chemical Information and Modeling, 51(9):2156–2163.

Schroeder, M., Kolodzik, A., Windshügel, B., Krepstakies, M., Priyadarshinic, P., Hauber, J., Rarey, M., Meier, C. (2010) Rational Drug Design - Screening and Synthesis of Potential Deoxyhypusine Synthase Inhibitors Targeting HIV-1 Replication .

Zaliani, A., Boda, K., Seidel, T., Herwig, A., Schwab, C. H., Gasteiger, J., Claußen, H., Lemmen, C., Degen, J., Pärn, J., Rarey, M. (2009) Second-generation de novo Design: A view from a medicinal chemist perspective . Journal of Computer-Aided Molecular Design, 23(8):593-602.

Steinbiss, S., Kurtz, S. (2012) A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences . IEEE/ACM Trans Comput Biol Bioinform, 9(2):345-357.

Hannemann, J., Meyer-Staeckling, S., Kemming, D., Alpers, I., Joosse, S.A., Pospisil, H., Kurtz, S., Görndt, J., Püschel, K., Riethdorf, S., Pantel, K., Brandt, B. (2011) Quantitative High-Resolution Genomic Analysis of Single Cancer Cells . PLoS ONE, 6(11):e26362.

Lippert, T., Schulz-Gasch, T., Roche, O., Guba, W., Rarey, M. (2011) De novo design by pharmacophore-based searches in fragment spaces . Journal of Computer-Aided Molecular Design, 25(10):931-945.

Rarey, M. (2011) Some thoughts on the A in computer-aided molecular design . Journal of Computer-Aided Molecular Design, 26(1):113-114.

Meyer, F., Kurtz, S., Backofen, R., Will, S., Beckstette, M. (2011) Structator: fast index-based search for RNA sequence-structure patterns . International German Conference on Bioinformatics. Highlight Track, Research Highlights

Schneider, N., Hindle, S., Lange, G., Klein, R., Albrecht, J., Briem, H., Beyer, K., Claußen, H., Gastreich, M., Lemmen, C., Rarey, M. (2011) Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function . Journal of Computer-Aided Molecular Design, 26(6):701-723.

Urbaczek, S., Kolodzik, A., Fischer, J. R., Lippert, T., Heuser, S., Schulz-Gasch, T., Rarey, M. (2011) NAOMI: On the Almost Trivial Task of Reading Molecules
from Different File formats . Journal of Chemical Information and Modeling, 51(12):3199-3207.

Rarey, M. (2012) Author Profile . ChemMedChem, 7(3):355.

Volkamer, A., Kuhn, D., Grombacher, T., Rippmann, F., Rarey, M. (2012) Combining Global and Local Measures for Structure-Based Druggability Predictions . Journal of Chemical Information and Modeling, 52(2):360-372.

Gonnella, G., Kurtz, S. (2012) Readjoiner: a fast and memory efficient string graph-based sequence assembler . BMC Bioinformatics, 13(82)

Volkamer, A., Kuhn, D., Rippmann, F., Rarey, M. (2012) DoGSiteScorer: A web-server for automatic binding site prediction, analysis, and druggability assessment . Bioinformatics, 28(15):2074–2075.

Schulz-Gasch, T., Schärfer, C., Guba, W., Rarey, M. (2012) TFD: Torsion Fingerprints As a New Measure To Compare Small
Molecule Conformations . Journal of Chemical Information and Modeling, 52(6):1499−1512.

Schneider, N., Klein, R., Lange, G., Rarey, M. (2012) Nearly no Scoring Function without a Hansch-Analysis . Molecular Informatics, 31(6-7):503–507.

Krohn, A., Diedler, T., Burkhardt, L., Mayer, P.-S., De Silva, C., Meyer-Kornblum, M., Kötschau, D., Tennstedt, P., Huang, J., Gerhäuser, C., Mader, M., Kurtz, S., Sirma, H., Saad, F., Steuber, T., Graefen, M., Plass, C., Sauter, G., Simon, R., Minner, S., Schlomm, T. (2012) Genomic Deletion of PTEN Is Associated with Tumor Progression and Early PSA Recurrence in ERG Fusion-Positive and Fusion-Negative Prostate Cancer . The American journal of pathology, 181(2):401-412.

Lessel, U., Wellenzohn, B., Fischer, J. R., Rarey, M. (2012) Design of Combinatorial Libraries for the Exploration of Virtual Hits
from Fragment Space Searches with LoFT . Journal of Chemical Information and Modeling, 52(2):373-379.

Ehrlich, H.-C., Rarey, M. (2012) Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2 . Journal of Cheminformatics, 4(13)

Ziegler, P., Chahoud, T., Wilhelm, T., Pällman, N., Braig, M., Wiehle, V., Ziegler, S., Schröder, M., Meier, C., Kolodzik, A., Rarey, M., Panse, J., Hauber, J., Balabanov, S., Brümmendorf, T. H. (2012) Evaluation of deoxyhypusine synthase inhibitors targeting BCR-ABL positive leukemias . Investigational New Drugs

Schomburg, K. T., Ardao, I., Götz, K., Rieckenberg, F., Liese, A., Zeng, A.-P., M., Rarey. (2012) Computational biotechnology: Prediction of competitive substrate inhibition
of enzymes by buffer compounds with protein-ligand docking . Journal of Biotechnology, 161:391-401.

Heinzerling, L., Klein, R., Rarey, M. (2012) Fast force field-based optimization of protein-ligand complexes with graphics processor . Journal of Computational Chemistry, 33(2):2554-2565.

Schwabe, T. (2012) Accurate and fast treatment of large molecular systems: Assessment of CEPA and pCCSD within the local pair natural orbital approximation . J. Comput. Chem., 33:2067-2072.

Schwabe, T.; Snesko, K.; Olsen, J.M.H.; Kongsted, K.; Christiansen, O.; Hättig, C. (2012) PERI-CC2: A Polarizable Embedded RI-CC2 Method . J. Chem. Theo. Comput., 8:3274-3283.

Matthies, M.C.; Bienert, S.; Torda, A.E. (2012) Dynamics in Sequence Space for RNA Secondary Structure Design . J. Chem. Theory Comput.

Perner, M.; Gonnella, G.; Hourdez, S.; Böhnke, S.; Kurtz, S.; Girguis, P. (2013) In-situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field . Environmental Microbiology , 15(5):1551-60.

Steinbiss, S; Kastens, S.; Kurtz, S. (2012) LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons . Mobile DNA, 3:18.

Harder, T., Borg, M., Bottaro, S., Boomsma, W., Olsson, S., Ferkinghoff-Borg, J., Hamelryck, T. (2012) An efficient null model for conformational fluctuations in proteins. . Structure:1028-1039.

Harder, T., Borg, M., Boomsma, W., Røgen, P., Hamelryck, T. (2012) Fast large-scale clustering of protein structures using Gauss integrals . Bioinformatics:510-515.

Olsson, S., Boomsma, W., Frellsen, J., Bottaro, S., Harder, T., Ferkinghoff-Borg, J., Hamelryck, T. Generative probabilistic models extend the scope of inferential structure determination . Journal of Magnetic Resonance:182-186.

Harder T., Boomsma W., Paluszewski M., Frellsen J., Johansson KE., Hamelryck T. (2010) Beyond rotamers: a generative, probabilistic model of side chains in proteins . BMC Bioinformatics:306 (1-13).

Harder T., Friedberg I., Kolodny R., Sitbon E., Li Z., Godzik A. (2006) Using an alignment of fragment strings for comparing protein structures . Bioinformatics:219-224.

Friedberg I., Harder T., Godzik A. (2006) JAFA: a protein function annotation meta-server . Nucleic Acids Res.:379-381.

Magbanua, E., Zivkovic, T., Hansen, B., Beschorner, N., Meyer, C., Lorenzn, I., Grötzinger, J., Hauber, J., Torda, A.E., Mayer, G., Rose-John, S., Hahn, U.
(2013) d(GGGT)4 and r(GGGU)4 are both HIV-1 inhibitors and interleukin-6 receptor aptamers . Landes Bioscience Journals: RNA Biology, 10(2)

Meanwell, N.A., Gastreich, M. Rarey, M.,Devereux, M., Popelier, P., Schneider, G., Willet, P. (2012) Perspectives from Medical Chemistry . In Bioisoteres in Medical Chemistry (Nathan Brown, ed.), pp. 217-230. Wiley-VCH .

Stierand, K., Harder, T., Marek, T., Hilbig, M., Lemmen, C., Rarey, M. (2012) The internet as scientific knowledge base: Navigating the chem-bio space . Molecular Informatics:543-546.

Kolodzik, A., Urbaczek, S., Rarey, M. (2012) Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies . Journal of Chemical Information and Modeling, 52(8):2013-2021.

Ehrlich, H.C., Volkamer, A., Rarey, M. (2012) Searching for Substructures in Fragment Spaces . Journal of Chemical Information and Modeling, 52(12):3181-3189.

Urbaczek, S., Kolodzik, A., Heuser, S., Groth, I., Rarey, M. (2013) Reading PDB: Perception of Molecules from 3D Atomic Coordinates . Journal of Chemical Information and Modeling, 53(1):76-87.

Volkamer, A., Kuhn, D., Rippmann, F., Rarey, M. (2013) Predicting enzymatic function from global binding site descriptors . Proteins: Structure, Function and Bioinformatics, 81(3):479-489.

Wiegels, T., Bienert, S., Torda, A.E. (2013) Fast alignment and comparison of RNA structures . Bioinformatics

Torda, A.E., Groves, M.R., Wedderhoff, I., Ortiz de Orué Lucana, D. (2013) Elucidation of haem-binding sites in the actinobacterial protein HbpS . FEMS Microbiology Letters

Schneider, N., Lange, G., Hindle, S., Klein, R., Rarey, M. (2013) A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function . Journal of Computer-Aided Molecular Design, 27(1):15-29.

Schomburg, K., Wetzer, L., Rarey, M. (2013) Interactive design of generic chemical patterns . Drug Discovery Today, 13:1-8.

von Behren, M., Volkamer, A., Henzler, A.M., Schomburg, K., Urbaczek, S., Rarey, M. (2013) Fast Protein Binding Site Comparison via an Index-Based Screening Technology . Journal of Chemical Information and Modeling, 53:411-422.

Schomburg, K., Stierand, K., Rarey, M. (2013) Informative Molekulare Visualisierung: Innovative grafische Darstellungen von Molekülmodellen veranschaulichen komplexe Zusammenhänge . BIOspektrum, 2:146-148.

Schärfer, C., Schulz-Gasch, T., Ehrlich, H.C., Guba, W., Rarey, M., Stahl, M. (2013) Torsion Angle Preferences in Drug-like Chemical Space: A Comprehensive Guide . Journal of Medicinal Chemistry, 56 (6):2016-28.

Schwabe, T. (2013) Systematic Study of the Basis Set Superposition Error in Core–Electron Correlation Effects . The Journal of Physical Chemistry A

Rarey, M., Schwabe, T. (2013) Jenseits von Google - Chemie im Computer- und Informationszeitalter . Praxis der Naturwissenschaften - Chemie in der Schule, 2(62):5-9.

Schwabe, T. (2013) Polarisierbare Einbettung . GIT Laborfachzeitschrift, 3(57):166-167.

Sneskov, K., Olsen, J. M. H., Schwabe, T., Hättig, C., Christiansen, O., Kongsted, J. (2013) Computational screening of one- and two-photon spectrally tuned channelrhodopsin mutants . Physical Chemistry Chemical Physics

Abdollahpour, H., Alawi, M., Beckstette, M., Seemanova, E., Komarek, V., Rosenberger, G., Kutsche, K. (2013) Exome sequencing identifies a homozygous frameshift mutation in AP481 in two siblings with severe intellectual disability, progressive spastic tetraplegia and microcephaly . Proc. of the 24th Jahrestagung der Deutschen Gesellschaft fuer Humangenetik, Dresden 2013

Ehrlich, H.-C., Henzler, A.M., Rarey, M. (2013) Searching for Recursively Defined Generic Chemical Patterns in Non-Enumerated Fragment Spaces . Journal of Chemical Information and Modeling, 53(7):1676-1688.

Schwabe, T. (2013) Comment on “Solvatochromic shifts of polar and non-polar molecules in ambient and supercritical water: A sequential quantum mechanics/molecular mechanics study including solute-solvent electron exchange-correlation” [J. Chem. Phys. 137, 214504 (2012)] . J. Chem. Phys., 138:217101.

Wirth, M., Volkamer, A., Zoete, V., Rippmann, F., Michielin, O., Rarey, M., Sauer, W.H.B. (2013) Protein pocket and ligand shape comparison and its application in virtual screening . Journal of Computer Aided Molecular Design, 27:511-524.

Simons, J.R., Mosisch, M., Torda, A.E., Hilterhaus, L. (2013) Site directed immobilization of glucose-6-phosphate dehydrogenase via thiol-disulfide interchange: Influence on catalytic activity of cysteines introduced at different positions . Journal of Biotechnology, 167:1-7.

Niebuhr, B., Kriebitzsch, N., Fischer, M., Behrens, K., Günther, T., Alawi, M., Bergholz, U., Müller, U., Roscher, S., Ziegler, M., Buchholz, F., Grundhoff, A., Stocking, C. (2013) Runx1 is essential at two stages of early murine B-cell development. . Blood: (Epub ahead of print).

Werner, S., Frey, S., Riethdorf, S., Schulze, C., Alawi, M., Kling, L., Vafaizadeh, V., Sauter, G., Terracciano, L., Schumacher, U., Pantel, K., Assmann, V. (2013) Dual Roles of the Transcription Factor Grainyhead-like 2 (GRHL2) in Breast Cancer . The Journal of Biological Chemistry: (Epub ahead of print).

Alawi, M., Mueller, D., Hoehne, M., Bock, CT., Mielke, M., Aepfelbacher, M., Fischer, N., Grundhoff, A.

(2013) Viral Metagenomics – next generation sequencing confirms the presence of multiple norovirus genotypes in stool samples collected during the largest gastroenteritis outbreak in Germany in fall 2012 . 23rd Annual Meeting of the Society for Virology

Gremme, G., Steinbiss, S., Kurtz, S. (2013) GenomeTools: A Comprehensive Software Library for Efficient Processing
of Structured Genome Annotations . IEEE/ACM Trans. Comput Biol. Bioinform., 10(3):645-56.

Meyer, F., Kurtz, S., Beckstette, M.
(2013) Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns
. BMC Bioinformatics(14):226.

Hilbig, M.; Urbaczek, S.; Groth, I.; Heuser, S.; Rarey, M. (2013) MONA - Interactive manipulation of molecule collections . Journal of Cheminformatics, 5 (38)

Schärfer, C.; Schulz-Gasch, T.; Hert, J.; Heinzerling, L. ; Schulz, B.; Inhester, T.; Stahl, M.; Rarey, M. (2013) CONFECT: Conformations from an Expert Collection of Torsion Patterns . ChemMedChem, 8:1690-1700.

Azzaoui, K.; Jacoby, E.; Senger, S.; Cuadrado Rodríguez, E.; Loza, M.; Zdrazil, B.; Pinto, M.; Williams, A.J.; de la Torre, V.; Mestres, J.; Pastor, M.; Taboureau, O.; Rarey, M.; Chichester, C.; Pettifer, S.; Blomberg, N.; Harland, L.; Williams-Jones, B.; Ecker, G.F. (2013) Scientific competency questions as the basis for semantically enriched open pharmacological space development . Drug Discovery Today, 18(17/18):843-852.

Nieselt K., Dietzsch J., Heinrich J., Pritzkau A., Mosisch M., Bartz D. (2010) Visuelle Analytik für Genexpressionsdaten . Datenbank-Spektrum, 31

Krohn-Molt, I., Wemheuer, B., Alawi, M., Poehlein, A., Güllert, S., Schmeisser, C., Pommerening-Röser, A., Grundhoff, A., Daniel, R., Hanelt, D., Streit, W.R. (2013) Metagenome survey of a multispecies and algae-associated biofilm reveals key elements of bacterial-algae interactions in photobioreactors . Applied and Environmental Microbiology, Epub ahead of print

Gremme, G., Steinbiss, S., Kurtz, S. (2013) GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations . German Conference on Bioinformatics 2013

Schröder, M., Kolodzik, A., Pfaff, K., Priyadarshini, P., Krepstakies, M., Hauber, J., Rarey, M., Meier, C. (2014) In silico Design, Synthesis and Screening of Novel Deoxyhypusine Synthase Inhibitors Targeting HIV-1 Replication . ChemMedChem, 9:940-952.

Volkamer, A., Rarey, M. (2014) Exploiting structural information for drug target assessment . Future Medicinal Chemistry, 6(3):319-331.

List, N. H., Pimenta, F. M., Holmegaard, L., Jensen, R. L., Etzerodt, M., Schwabe, T., Kongsted, J., Ogilby, P. R., Christiansen, O. (2014) Effect of chromophore encapsulation on linear and nonlinear optical properties: the case of “miniSOG”, a protein-encased flavin . Physical Chemistry Chemical Physics

Urbaczek, S., Kolodzik, A., Rarey, M. (2014) The Valence State Combination Model: A generic framework for handling tautomers and protonation states . Journal of Chemical Information and Modeling, 54(3):756-766.

Mader, M., Simon, R., Kurtz, S. (2014) FISH Oracle 2: A web server for integrative visualization of genomic data in cancer research . Journal of Clinical Bioinformatics, 4(1):5.

Schwabe, T. (2014) An isomeric reaction benchmark set to test if the performance of state-of-the-art density functionals can be regarded as independent of the external potential . Physical Chemistry Chemical Physics

Bietz, S.; Urbaczek, S.; Schulz, B.; Rarey, M. (2014) Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes . Journal of Cheminformatics, 6(12):1-12.

*Perner, M., *Gonnella, G., Kurtz, S., LaRoche, J. (* = joint first authors) (2014) Handling temperature bursts reaching 464 °C: different microbial strategies in the Sisters Peak hydrothermal chimney . Applied and Environmental Microbiology, 80(15):4585-4598.

Abdollahpour, H., Alawi, M., Kortüm, F., Beckstette, M., Seemanova, E. , Komárek, V., Rosenberger, G., Kutsche, K. (2014) An AP4B1 frameshift mutation in siblings with intellectual disability and spastic tetraplegia further delineates the AP-4 deficiency syndrome . Eur J Hum Genet., Epub ahead of print

Thiele, B., Kloster, M., Alawi, M., Indenbirken, D., Trepel, M., Grundhoff, A., Binder, M. (2014) Next-generation sequencing of peripheral B-lineage cells pinpoints the circulating clonotypic cell pool in multiple myeloma . Blood, Epub ahead of print

Fischer, N., Rohde, H., Indenbirken, D., Günther, T., Reumann, K., Lütgehetmann, M., Meyer, T., Kluge, S., Aepfelbacher, M., Alawi, M., Grundhoff, A. (2014) Rapid Metagenomic Diagnostics for Suspected Outbreak of Severe Pneumonia . Emerg Infect Dis

Schomburg, K.T.; Bietz, S.; Briem, H.; Henzler, A.M.; Urbaczek, S.; Rarey, M. (2014) Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening . Journal of Chemical Information and Modeling, 54(6):1676-1686.

Henzler, A.M., Urbaczek, S., Hilbig, M., Rarey, M. (2014) An integrated approach to knowledge-driven structure-based virtual screening . Journal of Computer-Aided Molecular Design, 28(9):927-39.

Bersch, B., Groves, M.R., Klare, J.P., Torda, A.E., Ortiz de Orué Lucana, D. (2014) Applications of Structural Biology and Bioinformatics in the Investigation of Oxidative Stress-Related Processes . In Systems Biology of Free Redicals annd Antioxidants (Laher, Ismail , ed.), pp. 505-534. Springer.

Inhester, T., Rarey, M. (2014) Protein-Ligand Interaction Databases: Advanced Tools to Mine Activity Data and Interactions on a Structural Level . WIREs Computational Molecular Science, 4(6):562-575.

Torda, A.E. (2014) Not assessing the efficiency of multiple sequence alignment programs . Algorithms for Molecular Biology, 9(18)

Schomburg, K.T.; Rarey, M. (2014) Benchmark Data Sets for Structure-Based Computational Target Prediction . Journal of Chemical Information and Modeling, 54(8):2261-2274.

Nagarajan, S., Hossan, T., Alawi, M., Najafova, Z., Idenbirken, D., Bedi, U., Taipaleenmäki, H., Ben-Batalla, I., Scheller, M., Loges, S., Knapp, S., Hesse, E., Chiang, CM., Grundhoff, A., Johnsen, SA. (2014) Bromodomain protein BRD4 is required for estrogen receptor-dependent enhancer activation and gene transcription. . Cell Rep, 8(2):460-9.

Kortüm, F., Abdollahpour, H., Alawi, M., Korenke, G.C., Seemanova, E., Tinschert, S., Zenker, M., Rosenberger, G., Kutsche, K. (2014) Exomsequenzierung zur Identifizierung von Krankheitsgenen für seltene Syndrome . Medizinische genetik, 25(2):246-254.

Deuse, T., Wang, D., Stubbendorff, M., Itagaki, R., Grabosch, A., Greaves L.C., Alawi, M., Gruenwald, A., Hu, X., Hua, X., Velden, J., Reichenspurner, H., Robbins R.C., Jaenisch, R., Weissman I.L. (Co-Senior author), Schrepfer, S. (Co-Senior author) (2014) SCNT-Derived ESCs with Mismatched Mitochondria Trigger an Immune Response in Allogeneic Hosts . Cell Stem Cell

Ilmberger, N., Güllert, S., Dannenberg, J., Rabausch, U., Torres, J., Wemheuer, B., Alawi, M., Poehlein, A., Chow, J., Turaev, D., Rattei, T., Schmeisser, C., Salomon, J., Olsen, P.B., Daniel, R., Grundhoff, A., Borchert, M.S., Streit, W.R. (2014) A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed Asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes. . PLoS One, 9(9):e106707.

Ortiz de Orue Lucana, D., Fedosov, S. N., Wedderhoff, I., Che, E. N., Torda, A. E. (2014) The Extracellular Heme-binding Protein HbpS from the Soil Bacterium Streptomyces reticuli Is an Aquo-cobalamin Binder . The Journal of Biological Chemistry, 289(49):34214-34228.

Schwabe, T., Beerepoot, M. T. P., Olsen, J. M. H., Kongsted, J. (2014) Analysis of computational models for an accurate study of electronic excitations in GFP . Physical Chemistry Chemical Physics, 17:2582-2588.

Schomburg, K., Rarey, M. (2014) What is the potential of structure-based target prediction methods? . Future Medicinal Chemistry, 6(18):1987 - 1989.

Yilmazer, N.D., Heitel, P., Schwabe, T., Korth, M. (2015) Benchmark of electronic structure methods for protein–ligand interactions based on high-level reference data . Journal of Theoretical and Computational Chemistry, 14(1):169-175.

Nittinger, E.; Schneider, N.; Lange, G.; Rarey, M. (2015) Evidence of Water Molecules—A Statistical Evaluation of Water Molecules Based on Electron Density . Journal of Chemical Information and Modeling, 55(4):771 - 783.

Schröder, H., Creon, A., Schwabe, T. (2015) Reformulation of the D3(Becke–Johnson) Dispersion Correction without Resorting to Higher than C6 Dispersion Coefficients . Journal of Chemical Theory and Computation, 11(7):3163-3170.

Kirchmair, J.; Göller, A. H.; Lang, D.; Kunze, J.; Testa, B.; Wilson, I. D.; Glen, R. C.; Schneider, G. (2015) Predicting drug metabolism: Experiment and/or computation? . Nature Reviews Drug Discovery, 14:387–404.

Richter, M.; Schumann, L.; Walther, E.; Hoffmann, A.; Braun, H.; Grienke, U.; Rollinger, J. M.; von Grafenstein, S.; Liedl, K. R.; Kirchmair, J.; Wutzler, P.; Sauerbrei, A.; Schmidtke, M. (2015) Complementary assays helping to overcome challenges for identifying neuraminidase inhibitors. . Future Virology , 10(2):77-88.

Walther, E.; Richter, M.; Xu, Z.; Kramer, C.; von Grafenstein, S.; Kirchmair, J.; Grienke, U.; Rollinger, J. M.; Liedl, K. R.; Slevogt, H.; Sauerbrei, A.; Saluz, H. P.; Pfister, W.; Schmidtke, M. (2015) Antipneumococcal activity of neuraminidase inhibiting artocarpin. . International Journal of Medical Microbiology , 305(3):289-97.

von Grafenstein, S.; Wallnöfer, H. G.; Kirchmair, J.; Fuchs, J. E.; Huber, R. G.; Spitzer, G.; Schmidtke, M.; Rollinger, J. M.; Liedl, K. R. (2015) Interface dynamics explain assembly dependency of influenza neuraminidase catalytic activity . Journal of Biomolecular Structure & Dynamics , 33 (1):104-120.

Tyzack, J. D.; Mussa, H. Y.; Williamson, M. J.; Kirchmair, J.; Glen, R. C. (2014) Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers . Journal of Cheminformatics, 29(6)

Rechfeld, F.; Gruber, P.; (shared 1st) Kirchmair, J.; Boehler, M.; Hauser, N.; Hechenberger, G.; Garczarczyk, D.; Lapa, G. B.; Preobrazhenskaya, M. N.; Goekjian, P.; Langer, T.; Hofmann, J., (2014) Thienoquinolines as novel disruptors of the PKCε/RACK2 protein-protein interaction. . Journal of Medicinal Chemistry, 57 (8):3235–3246.

Grienke, U.; Braun, H.; Seidel, N.; Kirchmair, J.; Richter, M.; Krumbholz, A.; von Grafenstein, S.; Liedl, K. R.; Schmidtke, M.; Rollinger, J. M., (2014) Computer-guided approach to access the anti-influenza activity of Licorice constituents . Journal of Natural Products , 77(3):563–570.

Kirchmair, J.; Williamson, M. J.; Afzal, A. M.; Tyzack, J. D.; Choy, A. P. K.; Howlett, A.; Rydberg, P.; Glen, R. C., (2013) FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes . Journal of Chemical Information and Modeling , 53:2896-2907.

Xuan, S.; Wang, M.; Kang, H.; Kirchmair, J.; Tan, L.; Yan, A. (2013) Support vector machine (SVM) models for predicting inhibitors of the 3’ processing step of HIV-1 integrase . Molecular Informatics , 32: 811-826.

Kirchmair, J.; Howlett, A.; Peironcely, J.; Murrell, D. S.; Williamson, M. J.; Adams, S. E.; Hankemeier, T.; van Buren, L.; Duchateau, G.; Klaffke, W.; Glen, R. C. (2013) How do metabolites differ from their parent molecules and how are they excreted? . Journal of Chemical Information and Modeling , 53(2):354-367.

Mak, L.; Liggi, S.; Tan, L.; Kusonmano , K.; Rollinger, J. M.; Koutsoukas, A.; Glen, R. C.; Kirchmair, J. (2013) Anti-cancer drug development: Computational strategies to identify and target proteins involved in cancer metabolism . Current Pharmaceutical Design, 19:532-577.

Distinto, S.; Esposito, F.; Kirchmair, J.; Cardia, M. C.; Gaspari, M.; Maccioni, E.; Alcaro, S.; Markt, P.; Wolber, G.; Zinzula, L.; Tramontano, E. (2012) Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint- and pharmacophore-based virtual screening approach . European Journal of Medicinal Chemistry, 50:216–229.

Kirchmair, J.; Williamson, M. J.; Tyzack, J. D.; Tan, L.; Bond, P. J.; Bender, A.; Glen, R. C., (2012) Computational prediction of metabolism: Sites, products, SAR, P450 enzyme dynamics and mechanisms . Journal of Chemical Information and Modeling 2012, 52:617-648.

Santos-Sierra, S.; Kirchmair, J.; Perna, A. M.; Reiß, D.; Kemter, K.; Röschinger, W.; Glossmann, H.; Gersting, S. W.; Muntau, A. C.; Wolber, G.; Lagler, F. (2012) Novel pharmacological chaperones that correct phenylketonuria in mice. . Human Molecular Genetics , 21:1877-1887.

Gleeson, M. P.; Modi, S.; Bender, A.; Marchese-Robinson, R. L.; Kirchmair, J.; Promkatkaew, M.; Hannongbua, S.; Glen, R. C. (2012) The challenges involved in modeling toxicity data in silico: A review. . Current Pharmaceutical Design, 18:1266-1291.

Distinto, S.; Yáñez, M.; Alcaro, S.; Cardia, M. C.; Gaspari, M.; Sanna, M. L.; Meleddu, R.; Ortuso, F.; Kirchmair, J.; Markt, P.; Bolasco, A.; Wolber, G.; Secci, D.; Maccioni, E. (2012) Synthesis and biological assessment of novel 2-thiazolylhydrazones and computational analysis of their recognition by monoamine oxidase B . European Journal of Medicinal Chemistry, 48:284-295.

Grienke, U.; Schmidtke, M.; von Grafenstein, S.; Kirchmair, J.; Liedl, K. R.; Rollinger, J. M. (2012) Influenza neuraminidase: A druggable target for natural products . Natural Product Reports, 29:11-36.

Koutsoukas, A.; Simms, B.; Kirchmair, J.; Bond, P. J.; Whitmore, A. V.; Zimmer, S.; Young, M. P.; Jenkins, J. L.; Glick, M.; Glen, R. C.; Bender, A. (2011) From in silico target prediction to multi-target drug design: Current databases, methods and applications . Journal of Proteomics, 74:2554-2574.

Rechfeld, F.; Gruber, P.; Hofmann, J.; Kirchmair, J. (2011) Modulators of protein-protein interactions – novel approaches in targeting protein kinases and other pharmaceutically relevant biomolecules . Current Topics in Medicinal Chemistry, 11(11):1305-1319.

Kirchmair, J.; Rollinger, J. M.; Liedl, K. R.; Seidel, N.; Krumbholz, A.; Schmidtke, M. (2011) Novel neuraminidase inhibitors: Identification, biological evaluation and investigations of the binding mode . Future Medicinal Chemistry, 3(4):437-450.

Kirchmair, J.; Distinto, S.; Liedl, K. R.; Markt, P.; Rollinger, J. M.; Schuster, D.; Spitzer, G.; Wolber, G. (2011) Development of anti-viral agents using molecular modelling and virtual screening techniques. . Infectious Disorders - Drug Targets, 11(1):64-93.

Schuster, D.; Kowalik, D.; Kirchmair, J.; Laggner, C.; Markt, P.; Aebischer-Gumy, C.; Ströhle, F.; Möller, G.; Wolber, G.; Wilckens, T.; Langer, T.; Odermatt, A.; Adamski, J. (2011) Identification of chemically diverse, novel inhibitors of 17beta-hydroxysteroid dehydrogenase type 3 and 5 by pharmacophore-based virtual screening . Journal of Steroid Biochemistry and Molecular Biology , 125(1-2):148-161.

Gruber, P.; Rechfeld, F.; Kirchmair, J.; Hauser, N.; Boehler, M.; Garczarczyk, D.; Langer, T.; Hofmann, J. (2011) Barbituric acid derivative BAS 02104951 inhibits PKCε, PKCη, PKCε/RACK2 interaction, Elk-1 phosphorylation in HeLa and PKCε and η translocation in PC3 cells following TPA-induction. . Journal of Biochemistry, 149(3):331-336.

Maenz, B.; Goetz, V.; Wunderlich, K.; Eisel, J.; Kirchmair, J.; Stech, J.; Stech, O.; Chase, G.; Frank, R.; Schwemmle, M. (2011) Disruption of the viral polymerase complex assembly as a novel approach to attenuate influenza A virus . Journal of Biological Chemistry, 286:8414-8424.

Spitzer, G.; Heiss, M.; Mangold, M.; Markt, P.; Kirchmair, J.; Wolber, G.; Liedl, K. R. (2010) One concept, three implementations of 3D pharmacophore-based virtual screening: Distinct coverage of chemical search space . Journal of Chemical Information and Modeling, 50(7):1241-1247.

Schuster, D.; Spetea, M.; Music, M.; Rief, S.; Fink, M.; Kirchmair, J.; Schütz, J.; Wolber, G.; Langer, T.; Stuppner, H.; Schmidhammer, H.; Rollinger, J. M. (2010) Morphinans and isoquinolines: acetylcholinesterase inhibition, pharmacophore modeling, and interaction with opioid receptors . Bioorganic & Medicinal Chemistry, 18:5071-5080.

Chimenti, F.; Secci, D.; Bolasco, A.; Chimenti, P.; Granese, A.; Carradori, S.; Maccioni, E.; Cardia, M. C.; Y·Òez, M.; Orallo, F.; Alcaro, S.; Ortuso, F.; Cirilli, R.; Ferretti, R.; Distinto, S.; Kirchmair, J.; Langer, T. (2010) Synthesis, semipreparative HPLC separation, biological evaluation, and 3D-QSAR of hydrazothiazole derivatives as human monoamine oxidase B Inhibitors . Bioorganic & Medicinal Chemistry, 18(14):5063-5070.

Schuster, D.; Kern, L.; Hristozov, D. P.; Terfloth, L.; Bienfait, B.; Laggner, C.; Kirchmair, J.; Grienke, U.; Wolber, G.; Langer, T. (2010) Applications of integrated data mining methods to exploring natural product space for acetylcholinesterase inhibitors . Combinatorial Chemistry & High Throughput Screening, 13:54-66.

Schuster, D.; Waltenberger, B.; Kirchmair, J.; Distinto, S.; Markt, P.; Stuppner, H.; Rollinger, J. M.; Wolber, G. (2010) Predicting cyclooxygenase inhibition by three-dimensional pharmacophoric profiling. Part I: Model generation, validation and applicability in ethnopharmacology . Molecular Informatics, 29(1-2):75-86.

Grienke, U.; Schmidtke, M.; Kirchmair, J.; Pfarr, K.; Wutzler, P.; Dürrwald, R.; Wolber, G.; Liedl, K. R.; Stuppner, H.; Rollinger, J. M. (2010) Antiviral potential and molecular insight into neuraminidase inhibiting diarylheptanoids from Alpinia katsumadai . Journal of Medicinal Chemistry, 53(2):778-786.

Tiikkainen, P.; Markt, P.; Wolber, G.; Kirchmair, J.; Distinto, S.; Poso, A.; Kallioniemi, O. (2009) Critical comparison of virtual screening methods against the MUV data set . Journal of Chemical Information and Modeling , 49(10):2168–2178.

Kirchmair, J.; Distinto, S.; Markt, P.; Schuster, D.; Spitzer, G. M.; Liedl, K. R.; Wolber, G. (2009) How to optimize shape-based virtual screening: Choosing the right query and including chemical information. . Journal of Chemical Information and Modeling, 49(3):678-692.

Spitzer, G. M.; Wellenzohn, B.; Markt, P.; Kirchmair, J.; Langer, T.; Liedl, K. R. (2009) Hydrogen-bonding patterns of minor groove-binder-DNA complexes reveal criteria for discovery of new scaffolds . Journal of Chemical Information and Modeling, 49(4):1063-1069.

Markt, P.; Feldmann, C.; Rollinger, J. M.; Raduner, S.; Schuster, D.; Kirchmair, J.; Distinto, S.; Spitzer, G. M.; Wolber, G.; Laggner, C.; Altmann, K. H.; Langer, T.; Gertsch, J. (2009) Discovery of novel CB2 receptor ligands by a pharmacophore-based virtual screening workflow . Journal of Medicinal Chemistry, 53(2):369-378.

Spitzer, G. M.; Fuchs, J. E.; Markt, P.; Kirchmair, J.; Wellenzohn, B.; Langer, T.; Liedl, K. R. (2008) Sequence-specific positions of water molecules at the interface between DNA and minor groove binders. . ChemPhysChem, 9(18):2766-2771.

Kirchmair, J.; Markt, P.; Distinto, S.; Schuster, D.; Spitzer, G. M.; Liedl, K. R.; Langer, T.; Wolber, G. (2008) The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery . Journal of Medicinal Chemistry, 51(22): 7021-7040.

Markt, P.; Petersen, R. K.; Flindt, E. N.; Krjstiansen, K.; Kirchmair, J.; Spitzer, G.; Distinto, S.; Schuster, D.; Wolber, G.; Laggner, C.; Langer, T. (2008) Discovery of novel PPAR ligands by a virtual screening approach based on pharmacophore modeling, 3D shape, and electrostatic similarity screening . Journal of Medicinal Chemistry, 51(20):6303-6317.

Kirchmair, J.; Distinto, S.; Schuster, D.; Spitzer, G.; Langer, T.; Wolber, G.
(2008) Enhancing drug discovery through in silico screening: Strategies to increase true positives retrieval rates . Current Medicinal Chemistry, 15(20):2040-2053.

Markt, P.; McGoohan, C.; Walker, B.; Kirchmair, J.; Feldmann, C. L.; De Martino, G.; Spitzer, G.; Distinto, S.; Schuster, D.; Wolber, G.; Laggner, C.; Langer, T. (2008) Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening . Journal of Chemical Information and Modeling, 48(8):1693-1705.

Schuster, D.; Nashev, L. G.; Kirchmair, J.; Laggner, C.; Wolber, G.;
Langer, T.; Odermatt, A. (2008) Discovery of nonsteroidal 17 beta-hydroxysteroid dehydrogenase 1 inhibitors by pharmacophore-based screening of virtual compound libraries . Journal of Medicinal Chemistry , 51(14):4188-4199.

Rollinger, J. M.; Steindl, T. M.; Schuster, D.; Kirchmair, J.; Anrain, K.; Ellmerer, E. P.; Langer, T.; Stuppner, H.; Wutzler, P.; Schmidtke, M. (2008) Structure-based virtual screening for the discovery of natural inhibitors for human rhinovirus coat protein . Journal of Medicinal Chemistry, 51(4):842-851.

Kirchmair, J.; Markt, P.; Distinto, S.; Wolber, G.; Langer, T. (2008) Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes? . Journal of Computer-Aided Molecular Design, 22(3-4):213-228.

Markt, P.; Schuster, D.; Kirchmair, J.; Laggner, C.; Langer, T. (2007) Pharmacophore modeling and parallel screening for PPAR ligands . Journal of Computer-Aided Molecular Design, 21(10-11):575-590.

Kirchmair, J.; Ristic, S.; Eder, K.; Markt, P.; Wolber, G.; Laggner, C.; Langer, T. (2007) Fast and efficient in silico 3D screening: Toward maximum computational efficiency of pharmacophore-based and shape-based approaches . Journal of Chemical Information and Modeling, 47:2182-2196.

Li, J.; Ehlers, T.; Sutter, J.; Varma-O\'Brien, S.; Kirchmair, J. (2007) CAESAR: A new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration . Journal of Chemical Information and Modeling, 47:1923-1932.

Kirchmair, J.; Wolber, G.; Laggner, C.; Langer, T. (2006) Comparative performance assessment of the conformational model generators Omega and Catalyst: A large-scale survey on the retrieval of protein-bound ligand conformations . Journal of Chemical Information and Modeling, 46(4):1848-1861.

Kirchmair, J.; Laggner, C.; Wolber, G.; Langer, T. (2005) Comparative analysis of protein-bound ligand conformations with respect to Catalyst\'s conformational space subsampling algorithms . Journal of Chemical Information and Modeling, 45(2):422-430.

Kirchmair, J.; (2014) Drug metabolism prediction . Wiley.

Chimenti, F.; Maccioni, E.; Cardia, M.C.; Secci, D.; Bolacso, A.; Alcaro, S.; Ortuso, F.; Orallo, F.; Kirchmair, J.; Markt, P.; Langer, T.; Distinto, S. (2009) Recent advances in monoamine oxidase B inhibitors design . :25-35.

Kirchmair, J. ; Spitzer, G. ; Liedl, K. R. (2011) Consideration of water and solvation effects in virtual screening . In Virtual Screening – Principles, Challenges, and Practical Guidelines (Sotriffer, C., ed.), pp. 263-289. Wiley-VCH.

Laggner, C.; Wolber, G.; Kirchmair, J.; Schuster, D.; Langer, T. (2008) Pharmacophore-based virtual screening in drug discovery . In Chemoinformatics approaches to virtual screening (Varnek, A. ; Tropsha, A., ed.), pp. 76-119. Royal Society of Chemistry.

Tan, Lu ; Kirchmair, J. (2014) Software for metabolism prediction . In Drug Metabolism Prediction (Kirchmair, J., ed.), Vol. 63, pp. 29-51. Wiley-VCH.

Schneider,N.; Volkamer,A.; Nittinger,E.; Rarey, M. (2015) Supporting Biocatalysis Research with Structural Bioinformatics . In Applied Biocatalysis: From Fundamental Science to Industrial Applications (in press) ( Liese, A.; Hilterhaus, L.; Kettling, U.; Antranikian, G. , ed.). Wiley-VCH.

Wagener, M.; Oellien, F.; Fechner, U.; Rarey, M. (2015) 10th ICCS/GCC Conference: 40 Years of Cheminformatics . Journal of Chemical Information and Modeling, 55(6):1087.

Bietz, S.; Rarey, M. (2015) ASCONA: Rapid Detection and Alignment of Protein Binding Site
Conformations . Journal of Chemical Information and Modeling, 55(8):1747–1756.

Bietz, S.; Schomburg, K. T.; Hilbig, M.; Rarey, M. (2015) Discriminative Chemical Patterns: Automatic and Interactive Design . Journal of Chemical Information and Modeling, 55(8):1535–1546.

Makarov, V. A.; Braun, H.; Richter, M.; Riabova, O. B.; Kirchmair, J.;
Kazakova, E. S.; Seidel, N.; Wutzler, P.; Schmidtke, M. (2015) Pyrazolopyrimidines: Potent inhibitors targeting the capsid of rhino-
and enteroviruses . ChemMedChem, 10:1629-1634.

Myllykoski, M., Seidel, L., Muruganandam, G., Raasakka, A., Torda, A.E., Kursula, P. (2015) Structural and functional evolution of 2´,3´-cyclic nucleotide 3´-phosphodiesterase . Brain Research:00701-5.

Marella, C., Torda, A.E., Schwudke, D. (2015) The LUX Score: A Metric for Lipidome Homology . PLOS Computational Biology, 10:1004511.

Bhargav, S.P., Vahokoski, J., Kallio, J.P., Torda, A.E., Kursula, P., Kursula, I. (2015) Two independently folding units of Plasmodium
profilin suggest evolution via gene fusion . Cellular and Molecular Life Sciences, 72(21):4193-4203.

Braun, H.;
Kirchmair, J.;
Williamson, M.J.;
Makarov, V.A.;
Riabova, O.B.;
Glen, R.C.;
Sauerbrei, A.;
Schmidtke, M. (2015) Molecular mechanism of a specific capsid binder resistance caused by mutations outside the binding pocket . Antiviral Research, 123:138-145.

Matthias Hilbig;
Matthias Rarey (2015) MONA 2: A Light Cheminformatics Platform for Interactive
Compound Library Processing . Journal of Chemical Information and Modeling, 55(10):2071–2078.

Thelemann, J.; Illarionov, B.; Barylyuk, K.;Geist, J.; Kirchmair, J.; Schneider, P.; Anthore, L.; Root, K.; Trapp, N.; Bacher, A.; Witschel, M.; Zenobi, R.; Fischer, M.; Schneider, G.; Diederich, F. (2015) Aryl bis-sulfonamide inhibitors of IspF from Arabidopsis thaliana and
Plasmodium falciparum . ChemMedChem, 10 (12):2090-2098.

Guba, W.; Meyder, A.; Rarey, M.; Hert, J. (2016) Torsion Library Reloaded: A New Version of Expert-Derived SMARTS rules
for Assessing Conformations of Small Molecules . Journal of Chemical Information and Modeling, 56(1):1-5.

Lang, T.; Flachsenberg, F.; von Luxburg, U.; Rarey, M. (2016) Feasibility of Active Machine Learning for Multiclass Compound
Classification . Journal of Chemical Information and Modeling, 56(1):12-20.

Bietz, S.; Rarey, M. (2016) SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles . Journal of Chemical Information and Modeling, 56(1):248-59.

Schwabe, T. (2015) Assessing Molecular Dynamics Simulations with Solvatochromism Modeling . Journal of Physical Chemistry B, 119(33):10693-10700.

Meyer, C., Hahn, U., Torda, A.E. (2013) RNA aptamer design . In De Novo Molecular Design (Gisbert Schneider, ed.), pp. 519-542

Kirchmair, J. (2015) Book Review: New Horizons in Predictive Drug Metabolism and Pharmacokinetics. Edited by Alan G. E. Wilson .

Walther, E.; Xu, Z.; Richter, M.; Kirchmair, J.; Grienke, U.; Rollinger, J.M.; Krumbolz, A.; Saluz, H.P.; Pfister, W.; Sauerbrei, A.; Schmidtke, M. (2016) Dual acting neuraminidase inhibitors open new opportunities to disrupt the lethal synergism between Streptococcus pneumoniae and influenza virus . Frontiers in Microbiology, 7 (357)

Bietz, S.; Fährrolfes, R.; Rarey, M. (2016) The Art of Compiling Protein Binding Site Ensembles . Molecular Informatics, 35(11/12):593-598.

Ortiz de Orué Lucana, D., Hickey, N., Hensel, M., Klare, J.P., Geremia, S., Tiufiakova, T., Torda, A.E. (2016) The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode . Frontiers in Microbiology

Grienke, U.; Richter, M.; Walther, E.; Hoffmann, A., Kirchmair, J.; Makarov, V.; Nietzsche, S.; Schmidtke, M.; Rollinger, J.M. (2016) Discovery of prenylated flavonoids with dual activity against influenza virus and Streptococcus pneumoniae . Scientific Reports, 27156

Sommer, K.; Friedrich, N.-O.; Bietz, S.; Hilbig, M.; Inhester, T.; Rarey, M: (2016) UNICON: A powerful and easy-to-use compound library converter . Journal of Chemical Information and Modeling, 56(6):1105–1111.

Lauck, F.; Rarey, M. (2016) FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption . Journal of Chemical Information and Modeling, 56(9):1641-1653.

von Behren, M.; Bietz, S.; Nittinger, E.; Rarey, M. (2016) mRAISE: an alternative algorithmic approach to ligand-based virtual screening . Journal of Computer-Aided Molecular Design, 30(8):583-594.

Schröder, H., Schwabe, T. (2016) Efficient Determination of Accurate Atomic Polarizabilities for Polarizeable Embedding Calculations . Journal of Computational Chemistry

Hoffmann, A.; Schade, D.; Kirchmair, J.; Clement, B.; Sauerbrei, A.; Schmidtke, M. (2016) Platform for determining the inhibition profile of neuraminidase inhibitors in an influenza virus N1 background . Journal of Virological Methods, 237:192-199.

Chen, Y.; Jin, H.; Zhang, L.; Liu, Z. (2016) Molecular models of different states of the human multidrug resistance protein 4 (MRP4/ABCC4) . Journal of Chinese Pharmaceutical Sciences, 25(6):428-437.

Xiaokaiti, Y.; Wu, H.; Chen, Y.; Yang, H.; Duan, J.; Li, X.; Tie, L.; Pan, Y.; Zhang, L.; Li, X. (2015) EGCG reverses human neutrophil elastase induced migration in A549 cells by directly binding with HNE and by regulating alpha1-AT . Scientific Reports, 5:11494.

Schwabe, T. (2016) General theory for environmental effects on (vertical) electronic excitation energies . The Journal of Chemical Physics, 145:154105.

Schwabe, T. (2016) Double hybrid density functional approximations . In Chemical Modelling (Michael Springborg, Jan-Ole Joswig, ed.), Vol. 13

Lauck, Florian; Rarey, Matthias (2013) Coping with Combinatorial Space in Molecular Design . In De novo Molecular Design, pp. 325-347

Inhester, T.; Bietz, S.; Hilbig, M.; Schmidt, R., Rarey, M. (2017) Index-based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces . Journal of Chemical Information and Modeling, 57(2):148-158.

Flachsenberg, F.; Andresen, N.; Rarey, M. (2017) RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases . Journal of Chemical Information and Modeling, 57(2):122-126.

Hoffmann, A.; Richter, M.; von Grafenstein, S.; Walther, E.; Xu, Z.; Schumann, L.; Grienke, U.; Mair, C.E.; Kramer, C.; Rollinger, J.M.; Liedl, K.R.; Schmidtke, M.; Kirchmair, J. (2017) Discovery and characterization of diazenylaryl sulfonic acids as inhibitors of viral and bacterial
neuraminidases . Frontiers in Microbiology, 8:Article 205.

Schröder, H., Hühnert, J., Schwabe, T. (2017) Evaluation of DFT-D3 dispersion corrections for various structural benchmark sets . AIP The Journal of Chemical Physics, 146(4)

Friedrich, N.-O.; Meyder, A.; Sommer, K.; Flachsenberg, F.; de Bruyn Kops, C.; Rarey, M.; Kirchmair, J. (2017) High-quality dataset of protein-bound ligand conformations and its application to benchmarking conformer ensemble generators . Journal of Chemical Information and Modeling, 57(3):529-539.

von Behren, M.; Rarey, M. (2017) Ligand-based Virtual Screening under Partial Shape Constraints . Journal of Computer-Aided Molecular Design, 31 (4):335-347.

Schwabe, Tobias (2017) Review of Proteinochromism Modeling in Computational Chemistry . Current Organic Chemistry, 21(10):856-871.

Schomburg, K.T.; Nittinger, E.; Meyder, A.; Bietz,S.; Schneider, N.; Lange, G.; Klein, R.; Rarey, M. (2017) Prediction of protein mutation effects based on dehydration and hydrogen bonding - A large-scale study . Proteins, 85(8):1550-1566.

Nittinger, E.; Inhester, T.; Bietz, S.; Meyder, A.; Schomburg, K.T.; Lange, G.; Klein, R.; Rarey, M. (2017) A Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces . Journal of Medicinal Chemistry, 60:4245-4257.

Gonnella, G.; Böhnke, S.; Indenbirken, D.; Garbe-Schönberg, D.; Seifert, R.; Mertens, C.; Kurtz, S.; Perner, M. (2016) Endemic hydrothermal vent species identified in the open ocean seed bank . Nature microbiology, 1:article number 16086

Gonnella G., Kurtz S. (2016) RGFA: powerful and convenient handling of assembly graphs . Peer J., 4:e2681

Fährrolfes, R.; Bietz, S.; Flachsenberg, F.; Meyder, A.; Nittinger, E.; Otto, T.; Volkamer, A.; Rarey, M. (2017) ProteinsPlus: a web portal for structure analysis of macromolecules . Nucleic Acids Research, 45:W337-W343.

de Bruyn Kops, Ch.; Friedrich, N.-O.; Kirchmair, J. (2017) Alignment-Based Prediction of Sites of Metabolism . Journal of Chemical Information and Modeling, 57(6):1258-1264.

Bietz, S.; Inhester, T.; Lauck, F.; Sommer, K.; von Behren, M.; Fährrolfes, R.; Flachsenberg, F.; Meyder, A.; Nittinger, E.; Otto, T.; Hilbig, M.; Schomburg, K.; Volkamer, A.; Rarey, M. (2017) From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library . Journal of Biotechnology, 261:207-214.

Giorgio Gonnella;
Stefan Kurtz (2017) GfaPy: a flexible and extensible software library for handling sequence graphs in Python . Bioinformatics(btx398)

Sicho, M.; de Bruyn Kops, C.; Stork, C.; Svozil, D.; Kirchmair, J. (2017) FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity . Journal of Chemical Information and Modeling, 57(8):1832-1846.

Chen, Y; de Bruyn Kops, C.; Kirchmair, J. (2017) Data Resources for the Computer-Guided Discovery of Bioactive Natural Products . Journal of Chemical Information and Modeling, 57 (9):2099-2111.

Inhester, T.; Nittinger, E.; Sommer, K.; Schmidt, P.; Bietz, S.; Rarey, M. (2017) NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures . Journal of Chemical Information and Modeling, 57(9):2132–2142.

Meyder, A.; Nittinger, E.; Lange, G.; Klein, R.; Rarey, M. (2017) Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures . Journal of Chemical Information and Modeling, 57(10):2437–2447.

Wagner, V.; Jantz, L.; Briem, H.; Sommer, K.; Rarey, M., Christ, C. (2017) Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation . ChemMedChem, 12(22):1866-1872.

Friedrich, N.-O.; de Bruyn Kops, Christina; Flachsenberg, F.; Sommer, K.; Rarey, M.; Kirchmair, J. (2017) Benchmarking Commercial Conformer Ensemble Generators . Journal of Chemical Information and Modeling, 57(11):2719-2728.

Stork, C.; Wagner, J.; Friedrich, N.-O.; de Bruyn Kops, C.; Sicho, M.; Kirchmair, J. (2018) Hit Dexter: A Machine-Learning Model for the Prediction of Frequent Hitters . ChemMedChem:in press.

Ehmki, E.S.R.; Rarey, M. (2018) Exploring Structure-Activity Relationships with Three-Dimensional Matched Molecular Pairs - A Review . ChemMedChem, 13(6):482-489.

Yuchen Han, Giorgio Gonnella, Nicole Adam, Axel Schippers, Lia Burkhardt, Stefan Kurtz, Ulrich Schwarz-Schampera, Henrike Franke, Mirjam Perner (2018) Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits . Scientific Reports, 8:10386.

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris & Johannes Köster - The Bioconda Team (2018) Bioconda: sustainable and comprehensive software distribution for the life sciences . Nature Methods, 15:475 - 476.

Chen, Y.; Garcia de Lomana, M.; Friedrich, N.-O.; Kirchmair, J. (2018) Characterization of the Chemical Space of Known and Readily Obtainable Natural Products . Journal of Chemical Information and Modeling

Nittinger, E.; Flachsenberg, F.; Bietz, S.; Lange, G.; Klein, R.; Rarey, M. (2018) Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples . Journal of Chemical Information and Modeling, 58(8):1625-1637.

Hochreiter, S.; Klambauer, G.; Rarey, M. (2018) Machine Learning in Drug Discovery . Journal of Chemical Information and Modeling, 58(9):1723-1724.

Meyder, A.; Kampen, S.; Sieg, J.; Fährrolfes, R.; Friedrich, N.-O.; Flachsenberg, F.; Rarey, M. (2018) StructureProfiler: An all-in-one Tool for 3D Protein Structure Profiling . Bioinformatics, 35(5):874-876.

Escribano, A.; Steenbock, T.; Stork, C.; Herrmann, C.; Heck, J. (2017) Why Are Dithienylethene-Linked Biscobaltocenes so Hard to Photoswitch? . ChemPhysChem, 18:596-609.

Stork, C.; Kirchmair, J. (2018) PAIN(S) relievers for medicinal chemists: how computational methods can assist in hit evaluation . Future Medicinal Chemistry, 10(13)

Nagammal Neelagandan, Giorgio Gonnella, Stefan Dang, Philipp C. Janiesch, Katharine K. Miller, Katrin Küchler, Rita F. Marques, Daniela Indenbirken, Malik Alawi, Adam Grundhoff, Stefan Kurtz, Kent E Duncan (2018) TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease . Nucleic Acids Research:gky972.

Sommer, K.; Flachsenberg, F.; Rarey, M. (2018) NAOMInext - Synthetically feasible fragment growing in a structure-based design context . European Journal of Medicinal Chemistry, 163:747-762.

Wilm, A.; Kühnl, J., Kirchmair, J. (2018) Computational approaches for skin sensitization prediction . Critical Reviews in Toxicology

Stork, C.; Chen, Y.; Sicho, M.; Kirchmair, J. (2019) Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters . Journal of Chemical Information and Modeling

Tyzack, J.D.; Kirchmair, J. (2018) Computational methods and tools to predict cytochrome P450 metabolism for drug discovery . Chemical Biology & Drug Design

Drexel, M. Kirchmair, J.; Santos-Sierra, S. (2018) INH14, a small-molecule urea derivative, inhibits the IKKα/β-dependent TLR inflammatory response . ChemBioChem

Chen, Y.; Stork, C.; Hirte, S.; Kirchmair, J. (2019) NP-Scout: Machine Learning Approach for the Quantification and Visualization of the Natural Product-Likeness of Small Molecules . Biomolecules, 9(43)

Galster, M.; Löppenberg, M.; Galla, F.; Börgel, F.; Agoglitta, O.; Kirchmair, J.; Holl, R. (2018) Phenylethylene glycol-derived LpxC inhibitors with diverse Zn2+-binding groups . Tetrahedron, 75:486-509.

Friedrich, N.-O.; Flachsenberg, F.; Meyder, A.; Sommer, K.; Kirchmair, J.; Rarey, M. (2019) Conformator: A Novel Method for the Generation of Conformer Ensembles . Journal of Chemical Information and Modeling, 59(2):731-742.

Sieg, J.; Flachsenberg, F.; Rarey, M. (2019) In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening . Journal of Chemical Information and Modeling(59):947-961.

Schmidt, R.; Ehmki, E.S.R.; Ohm, F.; Ehrlich, H.-C.; Mashychev, A.; Rarey, M. (2019) Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms . Journal of Chemical Information and Modeling, 59(6):2560-2571.

Ehmki, E.S.R.; Schmidt, R.; Ohm, F.; Rarey, M. (2019) Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis . Journal of Chemical Information and Modeling, 59(6):2572-2586.

Bellmann, L.; Penner, P.; Rarey, M. (2019) Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration . Journal of Chemical Information and Modeling, 59 (11):4625-4635.

Volkamer, A.; von Behren, M.; Bietz, S.; Rarey, M. (2018) Prediction, Analysis, and Comparison of Active Sites . In Applied Cheminformatics - Achievements and Future Opportunities. Wiley.

Kolodzik, A., Schneider, N.; Rarey, M. (2018) Structure-Based Virtual Screening . In Applied Cheminformatics - Achievements and Future Opportunities. Wiley.

Schöning-Stierand, K.; Diedrich, K.; Fährrolfes, R.; Flachsenberg, F.; Meyder, A.; Nittinger, E.; Steinegger, R.; Rarey, M. (2020) ProteinsPlus: interactive analysis of protein–ligand binding interfaces . Nucleic Acids Research, 48(W1):W48-W53.

Wilm, A.; Stork, C.; Bauer, C.; Schepky, A.; Kühnl, J.; Kirchmair, J. (2019) Skin Doctor: Machine Learning Models for Skin Sensitization Prediction that Provide Estimates and Indicators of Prediction Reliability . International Journal of Molecular Sciences, 20(19)

Orengo, C.; Velankar, S.; Wodak, S.; Zoete, V.; Bonvin, A.M.J.J.; Elofsson, A.; Feenstra, K.A.; Gerloff, D.L., Hamelryck, T.; Hancock, J.M.; Helmer-Citterich, M.; Hospital, A.; Orozco, M.; Perrakis, A.; Rarey, M.; Soares, C.; Sussmann, J.L.; Thornton, J.M.; Tuffery, P.; Tusnady, G.; Wierenga, R.; Salminen, T.; Schneider, B. (2020) A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) . F1000Research

Diedrich, K.; Graef, J.; Schöning-Stierand, K.; Rarey, M. (2020) GeoMine: interactive pattern mining of protein–ligand interfaces in the Protein Data Bank . Bioinformatics, 37(3):424-425.

Bellmann, L.; Penner, P.; Rarey, M. (2021) Topological Similarity Search in Large Combinatorial Fragment Spaces . Journal of Chemical Information and Modeling, 61(1):238-251.

Flachsenberg, F.; Meyder, A.; Sommer, K.; Penner, P.; Rarey, M. (2020) A Consistent Scheme for Gradient-Based Optimization of Protein–Ligand Poses . Journal of Chemical Information and Modeling

Schmidt, R.; Krull, F.; Heinzke, A.L.; Rarey, M. (2020) Disconnected Maximum Common Substructures under Constraints . Journal of Chemical Information and Modeling, 61(1):167-178.

Penner, P.; Martiny, V.; Gohier, A.; Gastreich, M.; Ducrot, P.; Brown, D.; Rarey, M. (2020) Shape-Based Descriptors for Efficient Structure-Based FragmentGrowing . Journal of Chemical Information and Modeling, 60:6269-6281.

Ehrt, C.; Krause, B.; Schmidt, R.; Ehmki, E.; Rarey, M. (2020) SMARTS.plus – A Toolbox for Chemical Pattern Design . Molecular Informatics, 39(12)

Flachsenberg, F.; Meyder, A.; Sommer, K.; Penner, P.; Rarey, M. (2012) A Consistent Scheme for Gradient-Based Optimization of Protein–Ligand Poses . Journal of Chemical Information and Modeling, 60(12):6502–6522.

Günther, S., Reinke, P.Y.A. et al (2021) Report X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease . Science, 372(6542):642-646.

Flachsenberg, F.; Rarey, M. (2021) LSLOpt: An open‐source implementation of the step‐length controlled LSL‐BFGS algorithm . Journal of Computational Chemistry, 42:1095-1100.

Graef, J.; Ehrt, C.; Diedrich, K.; Poppinga, M.; Ritter, N.; Rarey, M. (2021) Searching Geometric Patterns in Protein Binding Sites and Their Application to Data Mining in Protein Kinase Structures . Journal of Medicinal Chemistry, 65(2):1384-1395.

Schmidt, R.; Klein, R.; Rarey, M. (2021) Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces . Journal of Chemical Information and Modeling, 62(9):2133–2150.

Wilm, A.; Norinder, U.; Agea, M.I.; de Bruyn Kops, C.; Stork, C.; Kühnl, J.; Kirchmair, J. (2021) Skin Doctor CP: Conformal Prediction of the Skin Sensitization Potential of Small Organic Molecules . Chemical Research in Toxicology, 34(2):330-344.

Wilm, A.; Garcia de Lomana, M.; Stork, C.; Mathai, N.; Hirte, S.; Norinder, U.; Kühnl, J.; Kirchmair, J. (2021) Predicting the Skin Sensitization Potential of Small Molecules with Machine Learning Models Trained on Biologically Meaningful Descriptors . Pharmaceuticals, 14(8)

Günther, S.; Reinke, P.Y.A. et al (2021) X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease . Science, 372(6542):642-646.

Bellmann, L.; Penner, P.; Gastreich, M.; Rarey, M. (2022) Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs . Journal of Chemical Information and Modeling, 62(3):553–566.

Penner, P.; Guba, W.; Schmidt, R.; Meyder, A.; Stahl, M.; Rarey, M. (2022) The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare . Journal of Chemical Information and Modeling, 62(7):1644–1653.

Sieg, J.; Sandmeier, C.C.; Meents, A.; Lemmen, C.; Streit, W.R.; Rarey, M. (2022) Analyzing structural features of proteins from deep-sea organisms . Proteins: Structure, Function, and Bioinformatics, 90(8):1521-1537.

Warr, W.A.; Nicklaus, M.C.; Nicolaou, C.A.; Rarey, M. (2022) Exploration of Ultralarge Compound Collections for Drug Discovery . Journal of Chemical Information and Modeling, 62(9):2021–2034.

Schöning-Stierand, K.; Diedrich, K.; Ehrt, C.; Flachsenberg, F.; Graef, J.; Sieg, J.; Penner, P.; Poppinga, M.; Ungethüm, A.; Rarey, M. (2022) ProteinsPlus: a comprehensive collection of web-based molecular modeling tools . Nucleic Acids Research, 50(1):W611-W615.

Bellmann, L.; Klein, R.; Rarey, M. (2022) Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces . Journal of Chemical Information and Modeling, 62(11):2800-2810.

Harren, T.; Matter, H.; Hessler, G.; Rarey, M.; Grebner, C. (2022) Interpretation of Structure–Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence . Journal of Chemical Information and Modeling, 62(3):447-462.

Dolfus, U.; Briem, H.; Rarey, M. (2021) Synthesis-Aware Generation of Structural Analogues . Journal of Chemical Information and Modeling, 62(15):3565–3576.

Penner, P.; Martiny, V.; Bellmann, L.; Flachsenberg, F.; Gastreich, M.; Theret, I., Meyer, C.; Rarey, M. (2022) FastGrow: on‑the‑fly growing and its application to DYRK1A . Journal of Computer-Aided Molecular Design, 36(9)(639-651)

Hönig, S.M.N.; Lemmen, C.; Rarey, M. (2022) Small molecule superposition: A comprehensive overview on pose scoring of the latest methods . WIREs Computational Molecular Science

Meyenburg, C.; Dolfus, U.; Briem, H.; Rarey, M. (2022) Galileo: Three‑dimensional searching in large combinatorial fragment spaces on the example of pharmacophores . Journal of Computer-Aided Molecular Design, 37:1-16.

Hönig, S.M.N.; Lemmen, C.; Rarey, M. (2023) Small molecule superposition: A comprehensive overview on pose scoring of the latest methods . WIREs Computational Molecular Science

Gutermuth, T.; Sieg, J.; Stohn, T.; Rarey, M. (2023) Modeling with Alternate Locations in X-ray Protein Structures . Journal of Chemical Information and Modeling

Graef, J.; Ehrt, C.; Rarey, M. (2023) Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3 . Journal of Chemical Information and Modeling, 63(10):3128-3137.

Pletzer-Zelgert, J.; Ehrt, C.; Fender, I.; Griewel, A.; Flachsenberg, F.; Klebe, G.; Rarey, M. (2023) LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments . Structural Biology, 79(9):837-856.

Diedrich, K.; Krause, B.; Berg, O.; Rarey, M. (2023) PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams . Journal of Computer-Aided Molecular Design, 37:491–503.

Gonzalez-Ponce, K.; Horta Andrade, C.; Hunter, F.; Kirchmair, J.; Martinez-Mayorga, K.; Medina-Franco, J.L.; Rarey, M.; Tropsha, A.; Varnek, A.; Zdrazil, B. (2023) School of cheminformatics in Latin America . Journal of Cheminformatics, 15(82)

Dolfus, U.; Briem, H.; Gutermuth, T.; Rarey, M. (2023) Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures . Journal of Chemical Information and Modeling, 63(21):6587-6597.

Sieg, J. ; Rarey, M. (2023) Searching similar local 3D micro-environments in protein structure databases with MicroMiner . Briefings in Bioinformatics, 24(6)