Conformator: A Novel Method for the Generation of Conformer Ensembles

• DOI: 10.1021/acs.jcim.8b00704
• Publication Date: 2019-02-12T20:22:48Z
• Authors: Nils-Ole Friedrich; Florian Flachsenberg; Agnes Meyder; Kai Sommer; Johannes Kirchmair; Matthias Rarey
• Keywords: Conformational isomerism; Robustness

Computer-aided drug design methods such as docking, pharmacophore searching, 3D database and the creation of 3D-QSAR models need conformational ensembles to handle flexibility small molecules. Here, we present Conformator, an accurate effective knowledge-based algorithm for generating conformer ensembles. With 99.9% all test molecules processed, Conformator stands out by its robustness with respect input formats, molecular geometries, handling macrocycles. extended set rules sampling torsion angles, a novel macrocycle generation, new clustering assembly ensembles, reaches median minimum root-mean-square deviation (measured between protein-bound ligand conformations maximum 250 conformers) 0.47 Å no significant difference highest-ranked commercial OMEGA significantly higher accuracy than seven free algorithms, including RDKit DG algorithm. is freely available noncommercial use academic research.