Exploring the effect of PARP-1 flexibility in docking studies
We used REMD simulations to sample the conformational space of ligand-bound and unbound PARP-1. We observed the formation of an accessory pocket in the catalytic cleft of PARP-1. The selection of a PARP-1 conformation containing the accessory pocket improves the results of docking studies. This study highlights the beneficial effect of incorporating PARP-1 flexibility in docking studies of PARP-1 ligands.
parp poly(adp-ribose) polymerase remd replica exchange molecular dynamics pca principal components analysis rmsd root mean square deviation ef enrichment factor