Standard TABS Methodology
Standard TABS methodology overview.
Identification of torsions of interest:
For a given molecule, the torsions of interest are defined through a predefined set of SMARTS patterns [SCST13] [GWMA16] plus any additional non-trivial (atoms involved in the bond have at least one non-hydrogen neighbor) rotatable bonds.
Retrieving torsion information and fitting of the distributions to identify torsion states:
For each identified torsion, experimental-torsinal preferences in form of torsion-angle distributions are retrieved. The fits were performed by Riniker and Landrum [RSLG15].
Identification of torsion states (space discretization)
Based on the fitted distributions, torsion states are identified as local maxima in the distributions separated by local minima.
Assigning labels to conformers based on the torsion states
For a given conformer, each torsion is assigned a label corresponding to the torsion state it falls into. The collection of all torsion labels for a conformer constitutes its TABS label.
References
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. 56, 2016–2028 (2013).
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. 56, 1–5 (2016)
Riniker, S., Landrum, G. A.: Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. J. Chem. Inf. Model. 55, 2562–2574 (2015).