TorsionAnalyzer / TorsionPatternMiner

Overview

TorsionAnalyzer enables the analysis and inspection of torsion angles in small molecules. The tool is based on a collection of SMARTS patterns and rules derived from collections of high-quality crystal structures. The rotatable bonds of a molecule are assigned to three categories (relaxed, tolerable, strained) and colored accordingly. Users can evaluate large quantities of molecules with a given torsion library. The result table contains each torsion bond along with its corresponding torsion rule, angle, observed frequency, and quality category. The software displays a molecule in a conformation of interest and highlights bonds that exhibit geometrically unusual torsion angles. The software was developed in collaboration with F. Hoffmann-La Roche Ltd. in Basel and the ZBH - Center for Bioinformatics.

With TorsionAnalyzer, you can visually inspect the torsion angles of a given molecule and compare the angles to those observed in the Cambridge Structural Database (CSD) or Protein Data Bank (PDB) or recalculate angle frequencies based on your own dataset.

TorsionPatternMiner is an all-in-one command-line tool to populate torsion angle statistics for SMARTS torsion patterns for selected libraries of molecular conformations. SMARTScompare enables in-depth SMARTS pattern analysis. Users can apply the resulting torsion rules in many conformer generators such as Conformator, RDKit, or OMEGA.

Datasets

The most recent version of the Torsion Library derived from torsion angle statistics in the CSD and PDB can be downloaded at https://www.zbh.uni-hamburg.de/forschung/amd/datasets/torsion-library.html.

Software Availability

We are offering TorsionAnalyzer as a web service. Please visit https://torsions.zbh.uni-hamburg.de, upload your molecular conformations in SDF format, and visualize the torsion angles of the molecules in distributions of known angles for the chemical substructures.

TorsionAnalyzer is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download TorsionAnalyzer, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run TorsionAnalyzer. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Penner, P.; Guba, W.; Schmidt, R.; Meyder, A.; Stahl, M.; Rarey, M. The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. J Chem Inf Model 2022, 62 (7), 1644-1653. DOI: https://doi.org/10.1021/acs.jcim.2c00043
Guba, W.; Meyder, A.; Rarey, M.; Hert, J. Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules. J Chem Inf Model 2016, 56 (1), 1-5. DOI: https://doi.org/10.1021/acs.jcim.5b00522
Schärfer, C.; Schulz-Gasch, T.; Ehrlich, H. C.; Guba, W.; Rarey, M.; Stahl, M. Torsion angle preferences in druglike chemical space: a comprehensive guide. J Med Chem 2013, 56 (5), 2016-2028. DOI: https://doi.org/10.1021/jm3016816