{"id":"https://openalex.org/W2044172327","doi":"https://doi.org/10.1021/ci500020m","title":"<i>g_mmpbsa</i>\u2014A GROMACS Tool for High-Throughput MM-PBSA Calculations","display_name":"<i>g_mmpbsa</i>\u2014A GROMACS Tool for High-Throughput MM-PBSA Calculations","publication_year":2014,"publication_date":"2014-05-21","ids":{"openalex":"https://openalex.org/W2044172327","doi":"https://doi.org/10.1021/ci500020m","mag":"2044172327","pmid":"https://pubmed.ncbi.nlm.nih.gov/24850022"},"language":"en","primary_location":{"id":"doi:10.1021/ci500020m","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500020m","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/A5044914470","display_name":"Rashmi Kumari","orcid":"https://orcid.org/0000-0001-5435-4152"},"institutions":[{"id":"https://openalex.org/I152429107","display_name":"Jawaharlal Nehru University","ror":"https://ror.org/0567v8t28","country_code":"IN","type":"education","lineage":["https://openalex.org/I152429107"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Rashmi Kumari","raw_affiliation_strings":["School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India","School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India"],"affiliations":[{"raw_affiliation_string":"School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India","institution_ids":["https://openalex.org/I152429107"]},{"raw_affiliation_string":"School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India","institution_ids":["https://openalex.org/I152429107"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088808926","display_name":"Rajendra Kumar","orcid":"https://orcid.org/0000-0002-7268-9519"},"institutions":[{"id":"https://openalex.org/I152429107","display_name":"Jawaharlal Nehru University","ror":"https://ror.org/0567v8t28","country_code":"IN","type":"education","lineage":["https://openalex.org/I152429107"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Rajendra Kumar","raw_affiliation_strings":["School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India","School#R#of Computational and Integrative Sciences, Jawaharlal Nehru University, New#R#Delhi 110067, India"],"affiliations":[{"raw_affiliation_string":"School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India","institution_ids":["https://openalex.org/I152429107"]},{"raw_affiliation_string":"School#R#of Computational and Integrative Sciences, Jawaharlal Nehru University, New#R#Delhi 110067, India","institution_ids":["https://openalex.org/I152429107"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Open Source Drug Discovery Consortium","orcid":null},"institutions":[{"id":"https://openalex.org/I152429107","display_name":"Jawaharlal Nehru University","ror":"https://ror.org/0567v8t28","country_code":"IN","type":"education","lineage":["https://openalex.org/I152429107"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Open Source Drug Discovery Consortium","raw_affiliation_strings":["School#R#of Computational and Integrative Sciences, Jawaharlal Nehru University, New#R#Delhi 110067, India"],"affiliations":[{"raw_affiliation_string":"School#R#of Computational and Integrative Sciences, Jawaharlal Nehru University, New#R#Delhi 110067, India","institution_ids":["https://openalex.org/I152429107"]}]},{"author_position":"last","author":{"id":null,"display_name":"Andrew Lynn","orcid":null},"institutions":[{"id":"https://openalex.org/I152429107","display_name":"Jawaharlal Nehru University","ror":"https://ror.org/0567v8t28","country_code":"IN","type":"education","lineage":["https://openalex.org/I152429107"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Andrew Lynn","raw_affiliation_strings":["School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India"],"affiliations":[{"raw_affiliation_string":"School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India","institution_ids":["https://openalex.org/I152429107"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5044914470"],"corresponding_institution_ids":["https://openalex.org/I152429107"],"apc_list":null,"apc_paid":null,"fwci":52.4987,"has_fulltext":false,"cited_by_count":4681,"citation_normalized_percentile":{"value":0.99965113,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"54","issue":"7","first_page":"1951","last_page":"1962"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9984999895095825,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.7131597399711609},{"id":"https://openalex.org/keywords/accessible-surface-area","display_name":"Accessible surface area","score":0.6804273128509521},{"id":"https://openalex.org/keywords/solvent-models","display_name":"Solvent models","score":0.6188636422157288},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.603509247303009},{"id":"https://openalex.org/keywords/implicit-solvation","display_name":"Implicit solvation","score":0.5827591419219971},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5426495671272278},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4958980977535248},{"id":"https://openalex.org/keywords/sasa","display_name":"Sasa","score":0.4540579319000244},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.35671621561050415},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.34181827306747437},{"id":"https://openalex.org/keywords/solvent","display_name":"Solvent","score":0.31781381368637085},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.23941534757614136},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.21344685554504395}],"concepts":[{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.7131597399711609},{"id":"https://openalex.org/C11072593","wikidata":"https://www.wikidata.org/wiki/Q3622068","display_name":"Accessible surface area","level":2,"score":0.6804273128509521},{"id":"https://openalex.org/C2779455329","wikidata":"https://www.wikidata.org/wiki/Q22908915","display_name":"Solvent models","level":4,"score":0.6188636422157288},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.603509247303009},{"id":"https://openalex.org/C64147673","wikidata":"https://www.wikidata.org/wiki/Q6007318","display_name":"Implicit solvation","level":4,"score":0.5827591419219971},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5426495671272278},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4958980977535248},{"id":"https://openalex.org/C2776335000","wikidata":"https://www.wikidata.org/wiki/Q2322484","display_name":"Sasa","level":2,"score":0.4540579319000244},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.35671621561050415},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.34181827306747437},{"id":"https://openalex.org/C2780471494","wikidata":"https://www.wikidata.org/wiki/Q146505","display_name":"Solvent","level":2,"score":0.31781381368637085},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.23941534757614136},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.21344685554504395},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"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":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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/ci500020m","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500020m","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:24850022","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24850022","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":0.8500000238418579,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":101,"referenced_works":["https://openalex.org/W1572030366","https://openalex.org/W1845618662","https://openalex.org/W1967348240","https://openalex.org/W1967525398","https://openalex.org/W1969046853","https://openalex.org/W1975580333","https://openalex.org/W1976499671","https://openalex.org/W1977949865","https://openalex.org/W1978330227","https://openalex.org/W1978498560","https://openalex.org/W1979486475","https://openalex.org/W1988027147","https://openalex.org/W1994737524","https://openalex.org/W1994753033","https://openalex.org/W1997639796","https://openalex.org/W1998643862","https://openalex.org/W1999800992","https://openalex.org/W2000588442","https://openalex.org/W2000613080","https://openalex.org/W2004676220","https://openalex.org/W2007258535","https://openalex.org/W2009510905","https://openalex.org/W2009736039","https://openalex.org/W2011691446","https://openalex.org/W2012959003","https://openalex.org/W2014772558","https://openalex.org/W2015688756","https://openalex.org/W2016380176","https://openalex.org/W2016974200","https://openalex.org/W2018892220","https://openalex.org/W2020475659","https://openalex.org/W2021534482","https://openalex.org/W2023571753","https://openalex.org/W2024704410","https://openalex.org/W2026068349","https://openalex.org/W2029582401","https://openalex.org/W2030841140","https://openalex.org/W2032518125","https://openalex.org/W2033231433","https://openalex.org/W2033839720","https://openalex.org/W2035266068","https://openalex.org/W2036011280","https://openalex.org/W2037535298","https://openalex.org/W2041834854","https://openalex.org/W2043429268","https://openalex.org/W2045683699","https://openalex.org/W2047730466","https://openalex.org/W2048095530","https://openalex.org/W2048740445","https://openalex.org/W2049950136","https://openalex.org/W2054788798","https://openalex.org/W2057477511","https://openalex.org/W2059013803","https://openalex.org/W2060002448","https://openalex.org/W2060304556","https://openalex.org/W2065232574","https://openalex.org/W2065756075","https://openalex.org/W2065838297","https://openalex.org/W2067174909","https://openalex.org/W2073023478","https://openalex.org/W2074631079","https://openalex.org/W2075369230","https://openalex.org/W2075828031","https://openalex.org/W2075960258","https://openalex.org/W2078637473","https://openalex.org/W2078873851","https://openalex.org/W2084952324","https://openalex.org/W2086675373","https://openalex.org/W2090033012","https://openalex.org/W2091574192","https://openalex.org/W2092195398","https://openalex.org/W2093015919","https://openalex.org/W2096914244","https://openalex.org/W2103631613","https://openalex.org/W2106434473","https://openalex.org/W2110562802","https://openalex.org/W2112855704","https://openalex.org/W2118233996","https://openalex.org/W2125304058","https://openalex.org/W2128572087","https://openalex.org/W2131754023","https://openalex.org/W2132262459","https://openalex.org/W2140038584","https://openalex.org/W2142868265","https://openalex.org/W2143857558","https://openalex.org/W2144288821","https://openalex.org/W2144775933","https://openalex.org/W2147993766","https://openalex.org/W2150981663","https://openalex.org/W2156879354","https://openalex.org/W2160544821","https://openalex.org/W2161605421","https://openalex.org/W2163928645","https://openalex.org/W2166323701","https://openalex.org/W2166765429","https://openalex.org/W2169617040","https://openalex.org/W2169678694","https://openalex.org/W2171009743","https://openalex.org/W2327581403","https://openalex.org/W3004675605","https://openalex.org/W3102478570"],"related_works":["https://openalex.org/W4399502573","https://openalex.org/W2089507369","https://openalex.org/W1966793603","https://openalex.org/W4281748313","https://openalex.org/W2070280917","https://openalex.org/W4323037679","https://openalex.org/W2607010850","https://openalex.org/W2045242973","https://openalex.org/W1974433778","https://openalex.org/W2144871740"],"abstract_inverted_index":{"Molecular":[0],"mechanics":[1],"Poisson-Boltzmann":[2],"surface":[3,110],"area":[4,111],"(MM-PBSA),":[5],"a":[6,31,39,118,130,221],"method":[7,25],"to":[8,78,93,193,200,208],"estimate":[9,194],"interaction":[10,146],"free":[11,160],"energies,":[12],"has":[13,26,205],"been":[14,28,206],"increasingly":[15],"used":[16,192,207],"in":[17,34,212],"the":[18,45,55,68,107,137,140,144,195,201],"study":[19],"of":[20,67,139,148,164,168,223],"biomolecular":[21],"interactions.":[22],"Recently,":[23],"this":[24],"also":[27,190],"applied":[29],"as":[30,65,172],"scoring":[32],"function":[33],"computational":[35],"drug":[36],"design.":[37],"Here":[38],"new":[40],"tool":[41,90,141],"g_mmpbsa,":[42],"which":[43,120],"implements":[44],"MM-PBSA":[46],"approach":[47],"using":[48,129],"subroutines":[49],"written":[50],"in-house":[51],"or":[52],"sourced":[53],"from":[54],"GROMACS":[56],"and":[57,98,117,125,183],"APBS":[58],"packages":[59],"is":[60,77],"described.":[61],"g_mmpbsa":[62,188],"was":[63,186],"developed":[64],"part":[66],"Open":[69],"Source":[70],"Drug":[71],"Discovery":[72],"(OSDD)":[73],"consortium.":[74],"Its":[75],"aim":[76],"integrate":[79],"high-throughput":[80],"molecular":[81],"dynamics":[82],"(MD)":[83],"simulations":[84],"with":[85,156],"binding":[86,159,202,220],"energy":[87,147,196],"calculations.":[88],"The":[89,162],"provides":[91],"options":[92],"select":[94],"alternative":[95],"atomic":[96,173],"radii":[97],"different":[99],"nonpolar":[100,184],"solvation":[101],"models":[102,104,185],"including":[103],"based":[105],"on":[106],"solvent":[108,113],"accessible":[109,114],"(SASA),":[112],"volume":[115],"(SAV),":[116],"model":[119],"contains":[121],"both":[122],"repulsive":[123],"(SASA-SAV)":[124],"attractive":[126],"components":[127],"(described":[128],"Weeks-Chandler-Andersen":[131],"like":[132],"integral":[133],"method).":[134],"We":[135],"showcase":[136],"effectiveness":[138],"by":[142],"comparing":[143],"calculated":[145],"37":[149],"structurally":[150],"diverse":[151],"HIV-1":[152,213],"protease":[153,214],"inhibitor":[154],"complexes":[155],"their":[157],"experimental":[158],"energies.":[161],"effect":[163],"varying":[165],"several":[166],"combinations":[167],"input":[169],"parameters":[170],"such":[171],"radii,":[174],"dielectric":[175,180],"constant,":[176],"grid":[177],"resolution,":[178],"solute-solvent":[179],"boundary":[181],"definition,":[182],"investigated.":[187],"can":[189],"be":[191],"contribution":[197],"per":[198],"residue":[199],"energy.":[203],"It":[204],"identify":[209],"those":[210],"residues":[211],"that":[215],"are":[216],"most":[217],"critical":[218],"for":[219],"range":[222],"inhibitors.":[224]},"counts_by_year":[{"year":2026,"cited_by_count":181},{"year":2025,"cited_by_count":645},{"year":2024,"cited_by_count":616},{"year":2023,"cited_by_count":695},{"year":2022,"cited_by_count":720},{"year":2021,"cited_by_count":640},{"year":2020,"cited_by_count":414},{"year":2019,"cited_by_count":277},{"year":2018,"cited_by_count":195},{"year":2017,"cited_by_count":154},{"year":2016,"cited_by_count":81},{"year":2015,"cited_by_count":50},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2016-06-24T00:00:00"}