The ProteinsPlus web server aims to support life scientists in working with protein structures. Protein structures are the key to understanding protein function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. ProteinsPlus focuses on protein-ligand interactions. The server provides support for the initial steps of dealing with protein structures, namely structure search (MicroMiner, GeoMine), quality assessment (EDIAscorer, StructureProfiler), and preprocessing (Protoss). JAMDA enables users to perform an on-the-fly molecular docking of up to five molecules. The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced options, such as protein pocket detection (DoGSite), prediction of water molecule positions (WarPP), protein structure ensemble generation (SIENA), prediction of metal coordination (METALizer), the analysis of solvent channels in protein crystals (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.

The web service is available at https://proteins.plus/.

Publikationen

1. Ehrt, C.; Schulze, T.; Graef, J.; Diedrich, K.; Pletzer-Zelgert, J.; Rarey, M. (2025) ProteinsPlus: a publicly available resource for protein structure mining . Nucleic Acids Research, 53(W1):W478-W484.
2. 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.
3. 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.
4. 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.

SMARTSplus is the ultimate visualization and analysis platform for SMARTS patterns in cheminformatics. It provides access to five tools. 

SMARTSview revolutionizes the way chemical patterns are interpreted by transforming complex SMARTS expressions into intuitive, visual representations. Beyond visualization, SMARTSview also serves as a REST service, enabling seamless integration into web applications. Learn how to use the service here. 

SMARTScreate extends the power of SMARTSview with an interactive graphical editor and a graph mining component. It generates discriminative SMARTS patterns automatically based on molecule sets. It is available as an online service and integrated into our interactive SMARTSeditor, which is part of the NAOMI ChemBio Suite, making pattern discovery effortless. SMARTS patterns are crucial for compound filtering in molecular design. However, analyzing hundreds of structural filters manually is impractical. 

SMARTScompare and SMARTSsearch automate this task, providing deep pattern analysis and similarity search functionality. A stand-alone command-line tool is also available as part of our NAOMI ChemBio Suite. Expanding the power of SMARTS beyond molecules, ReactionSmartsCompare introduces comparison and search capabilities for reaction SMARTS patterns, facilitating retrosynthesis and molecule transformation analyses. 

SMARTSexplore is a specialized tool designed to visualize and analyze numerous collections of SMARTS expressions and their similarity relationships. Accessible directly from this platform, SMARTSexplore operates as an independent web server, featuring thousands of patterns sourced from more than ten distinct collections. Additionally, it enables users to upload custom SMARTS patterns for direct comparative analysis. 

The web service is available at https://smarts.plus/.

Publikationen

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

The AMD Software Server is the central download plattform for all our tools. After registration you get access to several programs related to cheminformatics and structure-based design. The software is for free for academic use and evaluation purposes.

The SmartChemist server shall enable anyone to discuss the chemistry of molecules competently and adequately. It matches common substructures and highlights them, providing their (trivial) names. The substructures highlighted are common functional groups, small (hetero)cycles, and some biologically relevant molecules.  As always, there are multiple different resources we used to build the SmartChemist, namely RDKit for the cheminformatics platform to enable doing this completely open source [1], a publication of Judson et al.,[2] the SMARTS examples page of the Daylight page as a starting point for common functional groups[3] (considerably altered), and PubChem[4,5] to automatically extract (hetero-)cycle names.

The web service is available at https://chemist.smarts.plus/.

[1] RDKit: Open-source cheminformatics. https://www.rdkit.org 
[2] Judson, P. N.; Ihlenfeldt, W. D.; Patel, H.; Delannee, V.; Tarasova, N.; Nicklaus, M. C. Adapting CHMTRN (CHeMistry TRaNslator) for a New Use. J Chem Inf Model 2020, 60 (7), 3336-3341. DOI: https://doi.org/10.1021/acs.jcim.0c00448
[3] https://daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html
[4] Kim, S.; Chen, J.; Cheng, T.; Gindulyte, A.; He, J.; He, S.; Li, Q.; Shoemaker, B. A.; Thiessen, P. A.; Yu, B.; et al. PubChem 2025 update. Nucleic Acids Res 2025, 53 (D1), D1516-D1525. DOI: https://doi.org/10.1093/nar/gkae1059
[5] PubChem. https://pubchem.ncbi.nlm.nih.gov/

Publikationen

1. Gutermuth, T.; Penner, P.; Sieg, J.; Dolfus, U.; Rarey, M. (2025) SmartChemist - Simplifying Communication About Organic Chemical Structures . Journal of Chemical Information and Modeling

FastGrow is a fast fragment-growing approach using a shape-based algorithm. It also features pharmacophore-like constraints, geometry optimization using JAMDA,[1] and built-in ensemble flexibility. Beginning with a fragment in the active site and an exit vector, FastGrow scans through thousands of possible fragment extensions in seconds.

The web service is available at https://fastgrow.plus/.

[1] Flachsenberg, F.; Ehrt, C.; Gutermuth, T.; Rarey, M. Redocking the PDB. J Chem Inf Model 2024, 64 (1), 219-237. DOI: https://doi.org/10.1021/acs.jcim.3c01573

Publikationen

1. Penner, P.; Martiny, V.; Gohier, A.; Gastreich, M.; Ducrot, P.; Brown, D.; Rarey, M. (2020) Shape-Based Descriptors for Efficient Structure-Based Fragment Growing . Journal of Chemical Information and Modeling, 60(12):6269-6281.

PoseView automatically generates two-dimensional diagrams of complexes with a focus on the interaction pattern between ligand and protein. Interactions between the molecules are estimated by a built-in interaction model that is based on atom types and simple geometric criteria. The quality of the resultant diagrams is comparable to hand-drawn examples from textbooks and scientific publications.

Publikationen

1. Stierand, K., Rarey, M. (2010) Drawing the PDB - Protein-Ligand Complexes in two Dimensions . Medicinal Chemistry Letters, 1(9):540-545.
2. Stierand, K., Rarey, M. (2007) From Modeling to Medicinal Chemistry: Automatic generation of two-dimensional complex diagrams . ChemMedChem, 2(6):853-860.
3. 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.

PPI Prediction Server classifies a protein-protein complex with regard to its interaction type into permanent, transient or crystal artifact. The discrimination is performed using two characteristics of the protein-protein complex, the hydrophobicity of the interface and the quotient of interface area ratios.

Protoss is a fully automated hydrogen prediction tool for protein-ligand complexes. It adds missing
hydrogen atoms to protein structures (PDB-format) and detects reasonable protonation states,
tautomers, and hydrogen coordinates of both protein and ligand molecules.

Publikationen

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