title: A novel scoring function for molecular docking.
abstract: We present a novel scoring function for docking of small molecules to protein binding sites. The scoring function is based on a combination of two main approaches used in the field, the empirical and knowledge-based approaches. To calibrate the scoring function we used an iterative procedure in which a ligand's position and its score were determined self-consistently at each iteration. The scoring function demonstrated superiority in prediction of ligand positions in docking tests against the commonly used Dock, FlexX and Gold docking programs. It also demonstrated good accuracy of binding affinity prediction for the docked ligands.
authors.affiliation: Algodign LLC, Bolshaya Sadovaya street 8, Moscow 123379, Russia. andrey.muryshev@algodign.com
authors.forename: A E
authors.initials: AE
authors.lastname: Muryshev
authors.forename: D N
authors.initials: DN
authors.lastname: Tarasov
authors.forename: A V
authors.initials: AV
authors.lastname: Butygin
authors.forename: O Yu
authors.initials: OY
authors.lastname: Butygina
authors.forename: A B
authors.initials: AB
authors.lastname: Aleksandrov
authors.forename: S M
authors.initials: SM
authors.lastname: Nikitin
mesh_terms: D001665:Binding Sites; D002151:Calorimetry; D015195:Drug Design; D007700:Kinetics; D008958:Models, Molecular; D008968:Molecular Conformation; D011506:Proteins / Q000737:chemistry*; D014961:X-Ray Diffraction
chemical_list: D011506:Proteins