GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking
| العنوان: | GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking |
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| المؤلفون: | Minkyung Baek, Chaok Seok, Hwan Won Chung, Woong-Hee Shin |
| المصدر: | Journal of Computer-Aided Molecular Design. 31:653-666 |
| بيانات النشر: | Springer Science and Business Media LLC, 2017. |
| سنة النشر: | 2017 |
| مصطلحات موضوعية: | 0301 basic medicine, Protein Conformation, Computer science, Design elements and principles, Ligands, Machine learning, computer.software_genre, 01 natural sciences, 03 medical and health sciences, 0103 physical sciences, Drug Discovery, Physical and Theoretical Chemistry, Databases, Protein, Binding affinities, Lead Finder, Binding Sites, 010304 chemical physics, business.industry, Proteins, Computer Science Applications, Molecular Docking Simulation, 030104 developmental biology, Protein–ligand docking, Research Design, Docking (molecular), Artificial intelligence, Decoy, business, computer, Software, Protein Binding |
| الوصف: | 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 . |
| تدمد: | 1573-4951 0920-654X |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4e50e5e404d90acb08af8228e85802f1 https://doi.org/10.1007/s10822-017-0030-9 |
| حقوق: | CLOSED |
| رقم الأكسشن: | edsair.doi.dedup.....4e50e5e404d90acb08af8228e85802f1 |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 15734951 0920654X |
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