{"id":"https://openalex.org/W2564155015","doi":"https://doi.org/10.1021/acs.jcim.6b00378","title":"New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein\u2013Protein Interfaces","display_name":"New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein\u2013Protein Interfaces","publication_year":2016,"publication_date":"2016-12-12","ids":{"openalex":"https://openalex.org/W2564155015","doi":"https://doi.org/10.1021/acs.jcim.6b00378","mag":"2564155015","pmid":"https://pubmed.ncbi.nlm.nih.gov/27936711"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00378","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00378","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029956522","display_name":"In\u00eas C. M. Sim\u00f5es","orcid":"https://orcid.org/0000-0002-9701-9431"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210138594","display_name":"Rede de Qu\u00edmica e Tecnologia","ror":"https://ror.org/04j14t006","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210138594"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"In\u00eas C. M. Sim\u00f5es","raw_affiliation_strings":["UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal"],"raw_orcid":"https://orcid.org/0000-0002-9701-9431","affiliations":[{"raw_affiliation_string":"UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085658463","display_name":"In\u00eas P. D. Costa","orcid":"https://orcid.org/0000-0002-4649-6393"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210138594","display_name":"Rede de Qu\u00edmica e Tecnologia","ror":"https://ror.org/04j14t006","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210138594"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"In\u00eas P. D. Costa","raw_affiliation_strings":["UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073148303","display_name":"Jo\u00e3o T. S. Coimbra","orcid":"https://orcid.org/0000-0001-9138-7498"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210138594","display_name":"Rede de Qu\u00edmica e Tecnologia","ror":"https://ror.org/04j14t006","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210138594"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o T. S. Coimbra","raw_affiliation_strings":["UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048088473","display_name":"Maria J. Ramos","orcid":"https://orcid.org/0000-0002-7554-8324"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210138594","display_name":"Rede de Qu\u00edmica e Tecnologia","ror":"https://ror.org/04j14t006","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210138594"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Maria J. Ramos","raw_affiliation_strings":["UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073540033","display_name":"Pedro Alexandrino Fernandes","orcid":"https://orcid.org/0000-0003-2748-4722"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"id":"https://openalex.org/I4210138594","display_name":"Rede de Qu\u00edmica e Tecnologia","ror":"https://ror.org/04j14t006","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210138594"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Pedro A. Fernandes","raw_affiliation_strings":["UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCIBIO, REQUIMTE, Departamento\rde Qu\u00edmica e Bioqu\u00edmica, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal","institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5073540033"],"corresponding_institution_ids":["https://openalex.org/I182534213","https://openalex.org/I4210138594"],"apc_list":null,"apc_paid":null,"fwci":2.8881,"has_fulltext":false,"cited_by_count":54,"citation_normalized_percentile":{"value":0.9126391,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"57","issue":"1","first_page":"60","last_page":"72"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/alanine-scanning","display_name":"Alanine scanning","score":0.9457793831825256},{"id":"https://openalex.org/keywords/alanine","display_name":"Alanine","score":0.7894301414489746},{"id":"https://openalex.org/keywords/mutagenesis","display_name":"Mutagenesis","score":0.6895020008087158},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5974340438842773},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.4541177749633789},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.44928431510925293},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3834327459335327},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3325783610343933},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.27195096015930176},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.22712615132331848},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18975836038589478},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.16025254130363464},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.1397986114025116},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.138624906539917},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0707336962223053},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.06320080161094666}],"concepts":[{"id":"https://openalex.org/C2780227090","wikidata":"https://www.wikidata.org/wiki/Q2636892","display_name":"Alanine scanning","level":5,"score":0.9457793831825256},{"id":"https://openalex.org/C2779856020","wikidata":"https://www.wikidata.org/wiki/Q218642","display_name":"Alanine","level":3,"score":0.7894301414489746},{"id":"https://openalex.org/C16318435","wikidata":"https://www.wikidata.org/wiki/Q149299","display_name":"Mutagenesis","level":4,"score":0.6895020008087158},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5974340438842773},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.4541177749633789},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.44928431510925293},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3834327459335327},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3325783610343933},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.27195096015930176},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.22712615132331848},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18975836038589478},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.16025254130363464},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.1397986114025116},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.138624906539917},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0707336962223053},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.06320080161094666}],"mesh":[{"descriptor_ui":"D000409","descriptor_name":"Alanine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000409","descriptor_name":"Alanine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000409","descriptor_name":"Alanine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6b00378","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00378","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:27936711","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27936711","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8399999737739563,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G2835248180","display_name":null,"funder_award_id":"NORTE-01-0145-FEDER000024","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G2947838375","display_name":null,"funder_award_id":"UID/MULTI/04378/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G353695567","display_name":null,"funder_award_id":"EXCL-II/QEQ-COM/0394/2012","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6967358005","display_name":null,"funder_award_id":"SFRH/BD/87434/2012","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G812551818","display_name":null,"funder_award_id":"POCI-01\u20130145- FEDER-007728","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":81,"referenced_works":["https://openalex.org/W1549357029","https://openalex.org/W1868384341","https://openalex.org/W1892998540","https://openalex.org/W1963982969","https://openalex.org/W1968984443","https://openalex.org/W1971166275","https://openalex.org/W1975580333","https://openalex.org/W1975734016","https://openalex.org/W1978330227","https://openalex.org/W1979366468","https://openalex.org/W1980933072","https://openalex.org/W1992899488","https://openalex.org/W1995993799","https://openalex.org/W1997509365","https://openalex.org/W2001969264","https://openalex.org/W2002797885","https://openalex.org/W2004145462","https://openalex.org/W2008235594","https://openalex.org/W2010143056","https://openalex.org/W2013376035","https://openalex.org/W2019054625","https://openalex.org/W2021309719","https://openalex.org/W2021534482","https://openalex.org/W2023370650","https://openalex.org/W2035266068","https://openalex.org/W2043666236","https://openalex.org/W2044199868","https://openalex.org/W2047399603","https://openalex.org/W2047693963","https://openalex.org/W2047993019","https://openalex.org/W2048263148","https://openalex.org/W2051543023","https://openalex.org/W2051710717","https://openalex.org/W2058052041","https://openalex.org/W2058521024","https://openalex.org/W2058527555","https://openalex.org/W2058653824","https://openalex.org/W2063109965","https://openalex.org/W2064811345","https://openalex.org/W2067007351","https://openalex.org/W2067174909","https://openalex.org/W2070254043","https://openalex.org/W2075828031","https://openalex.org/W2076790509","https://openalex.org/W2077546260","https://openalex.org/W2078361177","https://openalex.org/W2081832846","https://openalex.org/W2085405156","https://openalex.org/W2085902776","https://openalex.org/W2086928290","https://openalex.org/W2087574732","https://openalex.org/W2089831930","https://openalex.org/W2092780362","https://openalex.org/W2094316817","https://openalex.org/W2095719702","https://openalex.org/W2098888753","https://openalex.org/W2102640727","https://openalex.org/W2103449051","https://openalex.org/W2104555813","https://openalex.org/W2106140689","https://openalex.org/W2112194058","https://openalex.org/W2119080868","https://openalex.org/W2121753315","https://openalex.org/W2125758525","https://openalex.org/W2130479394","https://openalex.org/W2136206140","https://openalex.org/W2137167381","https://openalex.org/W2140796306","https://openalex.org/W2146109146","https://openalex.org/W2152495216","https://openalex.org/W2155030096","https://openalex.org/W2155589321","https://openalex.org/W2156879354","https://openalex.org/W2157807259","https://openalex.org/W2158072271","https://openalex.org/W2167398093","https://openalex.org/W2171356751","https://openalex.org/W2301930322","https://openalex.org/W2314118227","https://openalex.org/W2345189416","https://openalex.org/W2404280981"],"related_works":["https://openalex.org/W4236187932","https://openalex.org/W1989527063","https://openalex.org/W3201765258","https://openalex.org/W955763280","https://openalex.org/W2058959137","https://openalex.org/W2042655455","https://openalex.org/W2411175880","https://openalex.org/W2083415230","https://openalex.org/W2082874149","https://openalex.org/W2618513029"],"abstract_inverted_index":{"Knowing":[0],"how":[1],"proteins":[2],"make":[3],"stable":[4],"complexes":[5,71],"enables":[6],"the":[7,19,54,74,80,89,99,165,174,210,235],"development":[8],"of":[9,18,53,67,82,88,160,177,203,229,249,276,279],"inhibitors":[10],"to":[11,26,72,169,209],"preclude":[12],"protein\u2013protein":[13],"(P:P)":[14],"binding.":[15],"The":[16,86],"identification":[17,248],"specific":[20],"interfacial":[21],"residues":[22,183,188],"that":[23,173],"mostly":[24],"contribute":[25],"protein":[27,161],"binding,":[28],"denominated":[29],"as":[30],"hot":[31,250],"spots,":[32,251],"is":[33],"thus":[34],"critical.":[35],"Here,":[36],"we":[37,146,171],"refine":[38],"an":[39,137,150],"in":[40,79,214,273],"silico":[41],"alanine":[42,111],"scanning":[43],"mutagenesis":[44],"protocol,":[45],"based":[46],"on":[47],"a":[48,63,118,143,158,245],"residue-dependent":[49,75],"dielectric":[50,76,162,175],"constant":[51],"version":[52],"Molecular":[55],"Mechanics/Poisson\u2013Boltzmann":[56],"Surface":[57],"Area":[58],"method.":[59],"We":[60],"have":[61,147],"used":[62,78],"large":[64],"data":[65],"set":[66,159],"structurally":[68],"diverse":[69],"P:P":[70,101,287],"redefine":[73],"constants":[77,163,176],"determination":[81],"binding":[83,102,107,195,282],"free":[84,103,260],"energies.":[85],"accuracy":[87],"method":[90,242],"was":[91,212,222],"validated":[92],"through":[93],"comparison":[94],"with":[95,136,153,218,225],"experimental":[96],"data,":[97],"considering":[98],"per-residue":[100],"energy":[104,261],"(\u0394\u0394":[105],"G":[106,194],")":[108],"differences":[109],"upon":[110],"mutation.":[112],"Different":[113],"protocols":[114],"were":[115],"tested,":[116],"i.e.,":[117],"geometry":[119,219],"optimization":[120],"protocol":[121],"and":[122,141,181,184,254,265],"three":[123],"molecular":[124],"dynamics":[125],"(MD)":[126],"protocols:":[127],"(1)":[128],"one":[129],"using":[130],"explicit":[131,154,238],"water":[132,155],"molecules,":[133],"(2)":[134],"another":[135],"implicit":[138],"solvation":[139],"model,":[140],"(3)":[142],"third":[144],"where":[145],"carried":[148],"out":[149],"accelerated":[151],"MD":[152,226,236],"molecules.":[156],"Using":[157],"(within":[164],"range":[166],"from":[167],"1":[168],"20)":[170],"showed":[172],"7":[178],"for":[179,186,234,244,281],"nonpolar":[180],"polar":[182],"11":[185],"charged":[187],"(and":[189],"histidine)":[190],"provide":[191],"optimal":[192],"\u0394\u0394":[193],"predictions.":[196],"An":[197],"overall":[198],"mean":[199],"unsigned":[200],"error":[201],"(MUE)":[202],"1.4":[204],"kcal":[205,231],"mol":[206,232],"\u20131":[207,233],"relative":[208],"experiment":[211],"achieved":[213],"210":[215],"mutations":[216],"only":[217],"optimization,":[220],"which":[221],"further":[223],"reduced":[224],"simulations":[227],"(MUE":[228],"1.1":[230],"employing":[237],"solvent).":[239],"This":[240],"recalibrated":[241],"allows":[243],"better":[246],"computational":[247],"avoiding":[252],"expensive":[253],"time-consuming":[255],"experiments":[256],"or":[257],"thermodynamic":[258],"integration/":[259],"perturbation/":[262],"uBAR":[263],"calculations,":[264],"will":[266],"hopefully":[267],"help":[268],"new":[269],"drug":[270],"discovery":[271],"campaigns":[272],"their":[274],"quest":[275],"searching":[277],"spots":[278],"interest":[280],"small":[283],"drug-like":[284],"molecules":[285],"at":[286],"interfaces.":[288]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":3}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}