Otoya-Verastegui, Meliton, Flores-Sotelo, Willian Sebastian, Maita-Cruz, Yoni and Cotrina-Aliaga, Juan Digital transformation in the national fisheries development fund. International Journal of Early Childhood Special Education (INT-JECS), 2022, vol. 14, n. 3, pp. 7831-7845. [Journal article (Paginated)]
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English abstract
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-α-helical peptides and systematically improve pose prediction accuracy bynhancing 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 à for 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.
Item type: | Journal article (Paginated) |
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Keywords: | access to information, digitization modernization, electronic government, electronic medium, governance, information technology, online system, open date, public administration, public sector, services |
Subjects: | I. Information treatment for information services L. Information technology and library technology |
Depositing user: | MAGISTER MELITON OTOYA VERASTEGUI |
Date deposited: | 29 Jul 2022 20:32 |
Last modified: | 29 Jul 2022 20:32 |
URI: | http://hdl.handle.net/10760/43393 |
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