Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock.

ABSTRACT: Prediction of the bound configuration of small-molecule ligands that differ substantially from the cognate ligand of a protein co-crystal structure is much more challenging than re-docking the cognate ligand. Success rates for cross-docking in the range of 20-30 % are common. We present an approach that uses structural information known prior to a particular cutoff-date to make predictions on ligands whose bounds structures were determined later. The knowledge-guided docking protocol was tested on a set of ten protein targets using a total of 949 ligands. The benchmark data set, called PINC ("PINC Is Not Cognate"), is publicly available. Protein pocket similarity was used to choose representative structures for ensemble-docking. The docking protocol made use of known ligand poses prior to

SUBMITTER: Cleves AE 

PROVIDER: S-EPMC4464052 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature