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ZBH
ZBHZentrum für Bioinformatik

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Torsion Analyzer

Overview

The TorsionAnalyzer is a graphical user interface authored by Christin Schärfer enabling the visual inspection of torsion angles in molecules [1]. The software displays a molecule in a conformation of interest and highlights bonds which exhibit geometrically unusual torsion angles. The software is a result of a collaboration project between Roche, Basel and the ZBH. It is centered around an expert collection of torsion rules[1,2] derived from high quality crystallographic data from the Cambridge Structural Database.

With the TorsionAnalyzer, you can e.g.

  • visually inspect the torsion angles of a given molecule and compare the angles to the CSD
  • add or modify torsion rules, defined as SMARTS
  • recalculate angle frequencies based on your own data set
  • calculate conformations based on the given torsion library [3]
  • calculate the Torsion Fingerprint TFD of a molecule [4]

TorsionChecker[2] is a command-line tool to evaluate large quantities of molecules with a given torsion library. Each torsion bond with its matching torsion rule, angle, observed frequency in the CSD, and quality category are listed in a result table.

Software

The TorsionAnalyzer is freely available for academic users for Linux (64 and 32bit) as well as Mac and Windows as part of our NAOMI ChemBio Suite. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run the TorsionAnalyzer. All feedback is highly appreciated.

People and references

[1] 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.

[2] Guba, W.; Meyder, A.; Rarey, M.; Hert, J. (2015). Torsion Library Reloaded: A New Version of Expert-Derived SMARTS rules for Assessing Conformations of Small Molecules. Journal of Chemical Information and Modeling:accepted.

[3] 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.

[4] 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.