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Mayorga, M. G., Furgerson, K., Cook, K., Wardle, E. A., O'Hara, D. P., & Probst, C. J., et al. (2016). No 主観的健康感を中心とした在宅高齢者における 健康関連指標に関する共分散構造分析title. Journal of Chemical Information and Modeling, 6(2), 1689–1699. |
| Resource type: Journal Article DOI: 10.1017/CBO9781107415324.004 ID no. (ISBN etc.): 15523861 BibTeX citation key: Mayorga2016 View all bibliographic details  |
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| Attachments | URLs http://doi.wiley.c ... f%0Ausir.salford.a |
| Abstract |
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Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-$alpha{$}-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 Åfor the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.
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