The ProteinsPlus server offers a rich functionality related to protein structures. After uploading or selecting a PDB file, you can visualize the protein using the brand new NGL viewer, get an overview of small molecules bound and calculate various protein-related content. Protoss adds hydrogen atoms and optimizes the hydrogen bond network for you. Furthermore, it determines the tautomeric and protomeric states of the protein as well as small molecules contained. The DoGSiteScorer detects binding sites and estimates their druggability to name just two widely used services.
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.
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.
DogSiteScorer is an automated pocket detection and analysis tool which can be used for protein assessment. Predictions with DoGSiteScorer are based on calculated size, shape and chemical features of automatically predicted pockets, incorporated into a support vector machine for druggability estimation.
Note that the DoGSiteServer is no longer runing. The functionality is available as part of our new ProteinsPlus Server.
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.
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.
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.
PoseView (replaced by ProteinsPlus)
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.
Stierand, K., Rarey, M. (2010) Drawing the PDB - Protein-Ligand Complexes in two Dimensions . Medicinal Chemistry Letters, 1(9):540-545.
Stierand, K., Rarey, M. (2007) From Modeling to Medicinal Chemistry: Automatic generation of two-dimensional complex diagrams . ChemMedChem, 2(6):853-860.
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-Server (replaced by ProteinsPlus)
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.
The ChemBioNavigator allows the user to visualize the chemical and biological space of a set of molecules in a chemically-aware manner. The physicochemical properties of sets of molecules can be plotted against each other and each individual data point investigated further via direct links to original data sources. The ChemBioNavigator allows searching for structurally related molecules via a substructure pattern or general similarity search. Note that the ChemBioNavigator is currently switched off due to compatibility issues with the OpenPHACTS API.