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Assessment of Different Parameters on the Accuracy of Computational Alanine Scanning of Protein-Protein Complexes with the Molecular Mechanics/Generalized Born Surface Area Method
dc.contributor.author | Valdés-Tresanco M.E | |
dc.contributor.author | Valdés-Tresanco M.S | |
dc.contributor.author | Moreno E | |
dc.contributor.author | Valiente P.A. | |
dc.date.accessioned | 2023-10-24T19:23:55Z | |
dc.date.available | 2023-10-24T19:23:55Z | |
dc.date.created | 2023 | |
dc.identifier.issn | 15206106 | |
dc.identifier.uri | http://hdl.handle.net/11407/7886 | |
dc.description.abstract | Computational alanine scanning with the molecular mechanics generalized Born surface area (MM/GBSA) method constitutes a widely used approach for identifying critical residues at protein-protein interfaces. Despite its popularity, the MM/GBSA method still has certain drawbacks due to its dependence on many factors. Here, we performed a systematical study on the impact of four different parameters, namely, the internal dielectric constant, the generalized Born model, the entropic term, and the inclusion of structural waters on the accuracy of computational alanine scanning calculations with the MM/GBSA method. Our results show that the internal dielectric constant is the most critical parameter for getting accurate predictions. The introduction of entropy and interfacial water molecules decreased the quality of the predictions, while the generalized Born model had little to no effect. Considering the significance of the internal dielectric value, we proposed a methodology based on the energetic predominance of a particular set of amino acids at the protein-protein interface for selecting an appropriate value for this variable. We hope that these results serve as a guideline for future studies of protein-protein complexes using the MM/GBSA method. © 2023 American Chemical Society. | eng |
dc.language.iso | eng | |
dc.publisher | American Chemical Society | |
dc.relation.isversionof | https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146860147&doi=10.1021%2facs.jpcb.2c07079&partnerID=40&md5=366af1e499ddfa1f7cde5e0f7e629b68 | |
dc.source | J Phys Chem B | |
dc.source | Journal of Physical Chemistry B | eng |
dc.title | Assessment of Different Parameters on the Accuracy of Computational Alanine Scanning of Protein-Protein Complexes with the Molecular Mechanics/Generalized Born Surface Area Method | eng |
dc.type | Article | |
dc.rights.accessrights | info:eu-repo/semantics/restrictedAccess | |
dc.publisher.program | Ciencias Básicas | spa |
dc.type.spa | Artículo | |
dc.identifier.doi | 10.1021/acs.jpcb.2c07079 | |
dc.relation.citationvolume | 127 | |
dc.relation.citationissue | 4 | |
dc.relation.citationstartpage | 944 | |
dc.relation.citationendpage | 954 | |
dc.publisher.faculty | Facultad de Ciencias Básicas | spa |
dc.affiliation | Valdés-Tresanco, M.E., Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada, Computational Biology and Biomolecular Dynamics Laboratory, Center for Proteins Studies, Faculty of Biology, University of Havana, Havana, Havana, 10400, Cuba | |
dc.affiliation | Valdés-Tresanco, M.S., Faculty of Basic Sciences, University of Medellin, Antioquia, Medellin, 50031, Colombia | |
dc.affiliation | Moreno, E., Faculty of Basic Sciences, University of Medellin, Antioquia, Medellin, 50031, Colombia | |
dc.affiliation | Valiente, P.A., Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada, Computational Biology and Biomolecular Dynamics Laboratory, Center for Proteins Studies, Faculty of Biology, University of Havana, Havana, Havana, 10400, Cuba | |
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dc.type.version | info:eu-repo/semantics/publishedVersion | |
dc.identifier.reponame | reponame:Repositorio Institucional Universidad de Medellín | |
dc.identifier.repourl | repourl:https://repository.udem.edu.co/ | |
dc.identifier.instname | instname:Universidad de Medellín |
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