GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility
| العنوان: | GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility |
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| المؤلفون: | Jinsol Yang, Minkyung Baek, Chaok Seok |
| المصدر: | Journal of Computational Chemistry. 40:2739-2748 |
| بيانات النشر: | Wiley, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | 010304 chemical physics, Chemistry, Molecular Conformation, Proteins, Score, General Chemistry, Ligands, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Molecular Docking Simulation, Computational Mathematics, Crystallography, Molecular geometry, Protein–ligand docking, Docking (molecular), 0103 physical sciences, Software |
| الوصف: | Predicting conformational changes of both the protein and the ligand is a major challenge when a protein-ligand complex structure is predicted from the unbound protein and ligand structures. Herein, we introduce a new protein-ligand docking program called GalaxyDock3 that considers the full ligand conformational flexibility by explicitly sampling the ligand ring conformation and allowing the relaxation of the full ligand degrees of freedom, including bond angles and lengths. This method is based on the previous version (GalaxyDock2) which performs the global optimization of a designed score function. Ligand ring conformation is sampled from a ring conformation library constructed from structure databases. The GalaxyDock3 score function was trained with an additional bonded energy term for the ligand on a large set of complex structures. The performance of GalaxyDock3 was improved compared to GalaxyDock2 when predicted ligand conformation was used as the input for docking, especially when the input ligand conformation differs significantly from the crystal conformation. GalaxyDock3 also compared favorably with other available docking programs on two benchmark tests that contained diverse ligand rings. The program is freely available at http://galaxy.seoklab.org/softwares/galaxydock.html. © 2019 Wiley Periodicals, Inc. |
| تدمد: | 1096-987X 0192-8651 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0265d5a6acae8b205b5cb9780b73c56 https://doi.org/10.1002/jcc.26050 |
| حقوق: | CLOSED |
| رقم الأكسشن: | edsair.doi.dedup.....f0265d5a6acae8b205b5cb9780b73c56 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 1096987X 01928651 |
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