title: Evaluation of molecular docking using polynomial empirical scoring functions.
abstract: Molecular docking simulations are of pivotal importance for analysis of protein-ligand interactions and also an essential resource for virtual-screening initiatives. In molecular docking simulations several possible docked structures are generated, which create an ensemble of structures representing binary complexes. Therefore, it is crucial to find the best solution for the simulation. One approach to this problem is to employ empirical scoring function to identify the best docked structure. It is expected that scoring functions show a descriptive funnel-shaped energy surface without many false minima to impair the efficiency of conformational sampling. We employed this methodology against a test set with 300 docked structures. Docking simulations of these ligands against enzyme binding pocket indicated a funnel-shaped behavior of the complexation for this system. This review compares a set of recently proposed polynomial empirical scoring functions, implemented in a program called POLSCORE, with two popular scoring function programs (XSCORE and DrugScore). Overall comparison indicated that POLSCORE works better to predict the correct docked position, for the ensemble of docked structures analyzed in the present work.
authors.affiliation: Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.
authors.forename: Raquel
authors.initials: R
authors.lastname: Dias
authors.forename: Luis Fernando Saraiva Macedo
authors.initials: LF
authors.lastname: Timmers
authors.forename: Rafael Andrade
authors.initials: RA
authors.lastname: Caceres
authors.forename: Walter Filgueira
authors.initials: WF
authors.lastname: de Azevedo
mesh_terms: D051357:Cyclin-Dependent Kinase 2 / Q000737:chemistry; D036262:Empirical Research; D008024:Ligands; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D008024:Ligands; D011506:Proteins; D051357:Cyclin-Dependent Kinase 2