RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach.

ABSTRACT: RosettaLigand is a protein-small-molecule (ligand) docking software capable of predicting binding poses and is used for virtual screening of medium-sized ligand libraries. Structurally similar small molecules are generally found to bind in the same pose to one binding pocket, despite some prominent exceptions. To make use of this information, we have developed RosettaLigandEnsemble (RLE). RLE docks a superimposed ensemble of congeneric ligands simultaneously. The program determines a well-scoring overall pose for this superimposed ensemble before independently optimizing individual protein-small-molecule interfaces. In a cross-docking benchmark of 89 protein-small-molecule co-crystal structures across 20 biological systems, we found that RLE improved sampling efficiency in 62 cases, with a

SUBMITTER: Fu DY 

PROVIDER: S-EPMC5928483 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature