Baek, Minkyung Shin, Woong-Hee Chung, Hwan Won Seok, Chaok 2024-01-20T01:03:51Z 2024-01-20T01:03:51Z 2021-09-05 2017-07 0920-654X https://pubs.kist.re.kr/handle/201004/122590 Protein-ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein-ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein-ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html. English SPRINGER INCREMENTAL CONSTRUCTION ALGORITHM MOLECULAR DOCKING FLEXIBLE DOCKING TEST SET SWARM OPTIMIZATION GENETIC ALGORITHM BINDING-AFFINITY DESIGN PERFORMANCE VALIDATION GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking Article 10.1007/s10822-017-0030-9 1 JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, v.31, no.7, pp.653 - 666 JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 31 7 653 666 scie scopus 000405960300005 2-s2.0-85020550984 Biochemistry & Molecular Biology Biophysics Computer Science, Interdisciplinary Applications Biochemistry & Molecular Biology Biophysics Computer Science Article INCREMENTAL CONSTRUCTION ALGORITHM MOLECULAR DOCKING FLEXIBLE DOCKING TEST SET SWARM OPTIMIZATION GENETIC ALGORITHM BINDING-AFFINITY DESIGN PERFORMANCE VALIDATION Molecular docking Docking scoring function Decoy discrimination Energy parameter optimization Hybrid scoring function