… Scoring and numerical optimization of protein–ligand poses is an integral part of docking …
Here, we present a consistent scheme for pose scoring and gradient-based pose optimization. …

… set of ligands or to selecting the best poses between different … formal charges consistent with
those of known ligands. Hence, … makes use of a bond increment scheme. Some of the bond …

… a molecular weight distribution consistent with the empirical … functions to rank the ligand
poses retained in a docking … the double-decoupling scheme, the ligand is decoupled from …

… alignment and different scoring schemes. We describe a new … of ligand poses has been
restricted to clashing poses during … only a fixed number of consistent conformational states of the …

… –ligand complex, we treated the docking pose as the … ligand-binding poses in ten FKBP–ligand
complexes using gREST with the FB potential, starting from the individual docking poses…

… consistently and accurately for the small number of ligands considered here and gives free
energies consistent … restraint and integration scheme for physical consistency as described in …

… : predicting the binding poses of ligands using a docking … LIE scheme, may be useful to
compensate for some of these limitations. Indeed, a simple scaling scheme seems to consistently …

… Interestingly, this fast and simple rescoring scheme provided the … , the GRIM–HYDE scoring
scheme is accurate and fast … which docking poses are of good quality, consistent failures in …

… is the belief that if the correct poses for multiple ligands can be consistently identified, then a
… MM-GBSA binding free energy prediction scheme, we used the same 855 membered data …

… It also demonstrates that the suggested optimal IRFPG value is very consistent across the …
Randomly selected ranking scheme: 100 poses were randomly selected from the ensemble …