ASCONA is a fully automated command line tool for generating sequence alignments and superpositions of protein binding sites. Itisgeared to the alignment of alternative protein conformations and especially addresses the tasks of dealing with highly flexible backbone regions, detecting multiple occurrences of a binding site in oligomeric structures, and coping with arbitrary annotation inconsistencies and structural artifacts.

ASCONA

Publikationen

1. 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.

Protoss is a fully automated hydrogen atom placement tool for protein-ligand complexes. It adds missing hydrogen atoms to protein structures and detects reasonable protonation states, tautomeric states, and hydrogen coordinates of both protein and ligand molecules by optimizing the hydrogen bond network.

Protoss

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)

SIENA is a software pipeline enabling the fully automated construction of protein structure ensembles from the PDB. Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and superimposed. SIENA also handles complicated cases, such as comparing binding sites at protein domain interfaces or within multimeric proteins.

SIENA

Publikationen

1. Bietz, S.; Rarey, M. (2016) SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles . Journal of Chemical Information and Modeling, 56(1):248-259.

SMARTSminer was developed to generate SMARTS patterns that distinguish molecules from two different sets. It can, for example, create SMARTS patterns that match active molecules of a target of interest but do not match inactive molecules. Besides screening, the SMARTSminer technology can also provide valuable insights into typical patterns of frequent hitters or elucidate differences between sets of molecules binding to different target types.

SMARTSminer

Publikationen

1. 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.