{"id":"https://openalex.org/W2158534713","doi":"https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b","title":"Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function","display_name":"Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function","publication_year":1998,"publication_date":"1998-11-15","ids":{"openalex":"https://openalex.org/W2158534713","doi":"https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b","mag":"2158534713"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5011245839","display_name":"Garrett M. Morris","orcid":"https://orcid.org/0000-0003-1731-8405"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Garrett M. Morris","raw_affiliation_strings":["Department of Molecular Biology, MB-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037-1000"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, MB-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037-1000","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040337866","display_name":"David S. Goodsell","orcid":"https://orcid.org/0000-0002-5932-2130"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David S. Goodsell","raw_affiliation_strings":["Department of Molecular Biology, MB-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037-1000"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, MB-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037-1000","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010286152","display_name":"Robert S. Halliday","orcid":null},"institutions":[{"id":"https://openalex.org/I1324840837","display_name":"Hewlett-Packard (United States)","ror":"https://ror.org/059rn9488","country_code":"US","type":"company","lineage":["https://openalex.org/I1324840837"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert S. Halliday","raw_affiliation_strings":["Hewlett-Packard, San Diego, California"],"affiliations":[{"raw_affiliation_string":"Hewlett-Packard, San Diego, California","institution_ids":["https://openalex.org/I1324840837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000392051","display_name":"Ruth Huey","orcid":null},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruth Huey","raw_affiliation_strings":["Department of Molecular Biology, MB-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037-1000"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, MB-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037-1000","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102842741","display_name":"William E. Hart","orcid":"https://orcid.org/0000-0002-6849-2780"},"institutions":[{"id":"https://openalex.org/I4210104735","display_name":"Sandia National Laboratories","ror":"https://ror.org/01apwpt12","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210104735"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William E. Hart","raw_affiliation_strings":["Applied Mathematics Department, Sandia National Laboratories, Albuqurque, New Mexico"],"affiliations":[{"raw_affiliation_string":"Applied Mathematics Department, Sandia National Laboratories, Albuqurque, New Mexico","institution_ids":["https://openalex.org/I4210104735"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004299489","display_name":"Richard K. Belew","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard K. Belew","raw_affiliation_strings":["Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058956938","display_name":"Arthur J. Olson","orcid":"https://orcid.org/0000-0003-0558-4618"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Arthur J. Olson","raw_affiliation_strings":["Department of Molecular Biology, MB-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037-1000"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, MB-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037-1000","institution_ids":["https://openalex.org/I123431417"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5058956938"],"corresponding_institution_ids":["https://openalex.org/I123431417"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":51.3646,"has_fulltext":false,"cited_by_count":10764,"citation_normalized_percentile":{"value":0.99956503,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"19","issue":"14","first_page":"1639","last_page":"1662"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9966999888420105,"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/T11440","display_name":"Click Chemistry and Applications","score":0.9871000051498413,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.7357812523841858},{"id":"https://openalex.org/keywords/simulated-annealing","display_name":"Simulated annealing","score":0.7017162442207336},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5299466848373413},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.524779736995697},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5004682540893555},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.4808964729309082},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3963449001312256},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3421996533870697},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3316393494606018},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24514836072921753},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.14542773365974426},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.13761991262435913}],"concepts":[{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.7357812523841858},{"id":"https://openalex.org/C126980161","wikidata":"https://www.wikidata.org/wiki/Q863783","display_name":"Simulated annealing","level":2,"score":0.7017162442207336},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5299466848373413},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.524779736995697},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5004682540893555},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.4808964729309082},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3963449001312256},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3421996533870697},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3316393494606018},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24514836072921753},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.14542773365974426},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.13761991262435913},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.113.6936","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.113.6936","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.daimi.au.dk/~cstorm/courses/AiB/e04/www-aibtas/papers/autodock_morris_1998.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.471.5900","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.471.5900","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://hidra1.cbm.uam.es/publications/teaching/curso_verano_uah_2011/autodock4.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8299999833106995}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":72,"referenced_works":["https://openalex.org/W1496040402","https://openalex.org/W1497256448","https://openalex.org/W1534150290","https://openalex.org/W1555837804","https://openalex.org/W1582109070","https://openalex.org/W1650426659","https://openalex.org/W1656114533","https://openalex.org/W1964958542","https://openalex.org/W1965269646","https://openalex.org/W1966041739","https://openalex.org/W1970658820","https://openalex.org/W1977467384","https://openalex.org/W1979046104","https://openalex.org/W1979234818","https://openalex.org/W1983066351","https://openalex.org/W1988111902","https://openalex.org/W1988548997","https://openalex.org/W1991161477","https://openalex.org/W1999271199","https://openalex.org/W1999968212","https://openalex.org/W2001130582","https://openalex.org/W2005651680","https://openalex.org/W2008517160","https://openalex.org/W2012667948","https://openalex.org/W2019962781","https://openalex.org/W2021534482","https://openalex.org/W2024060531","https://openalex.org/W2024243556","https://openalex.org/W2025277814","https://openalex.org/W2027640169","https://openalex.org/W2034953645","https://openalex.org/W2035266068","https://openalex.org/W2040591694","https://openalex.org/W2041654633","https://openalex.org/W2051163038","https://openalex.org/W2051628563","https://openalex.org/W2051654117","https://openalex.org/W2052906698","https://openalex.org/W2056760934","https://openalex.org/W2060130346","https://openalex.org/W2062598572","https://openalex.org/W2067455153","https://openalex.org/W2067872997","https://openalex.org/W2071158076","https://openalex.org/W2072759559","https://openalex.org/W2073277085","https://openalex.org/W2075662564","https://openalex.org/W2076503226","https://openalex.org/W2079243965","https://openalex.org/W2080653934","https://openalex.org/W2084891561","https://openalex.org/W2092019850","https://openalex.org/W2110681410","https://openalex.org/W2114621223","https://openalex.org/W2120051461","https://openalex.org/W2121954997","https://openalex.org/W2122199548","https://openalex.org/W2123754662","https://openalex.org/W2123859926","https://openalex.org/W2142183404","https://openalex.org/W2154151185","https://openalex.org/W2161117347","https://openalex.org/W2162166182","https://openalex.org/W2324777999","https://openalex.org/W2412713395","https://openalex.org/W2431747270","https://openalex.org/W2473061264","https://openalex.org/W3129191898","https://openalex.org/W3209002371","https://openalex.org/W4253211029","https://openalex.org/W4293003482","https://openalex.org/W4301173492"],"related_works":["https://openalex.org/W2058674645","https://openalex.org/W1594539819","https://openalex.org/W2766845742","https://openalex.org/W2007257620","https://openalex.org/W4213038553","https://openalex.org/W2130867670","https://openalex.org/W1984029386","https://openalex.org/W4312202637","https://openalex.org/W2136513242","https://openalex.org/W2336040088"],"abstract_inverted_index":{"A":[0],"novel":[1],"and":[2,21,61,79,84,105,128,139,200,212],"robust":[3],"automated":[4],"docking":[5],"method":[6,40,121],"that":[7,30,101,129],"predicts":[8],"the":[9,32,80,103,118,130,135,142,169,204],"bound":[10],"conformations":[11],"of":[12,45,51,90,115,126,141,154,168,175,179,193],"flexible":[13],"ligands":[14,111],"to":[15],"macromolecular":[16],"targets":[17],"has":[18],"been":[19],"developed":[20],"tested,":[22],"in":[23,47,88,123,173,219],"combination":[24],"with":[25,112,160],"a":[26,42,75,152,176,189],"new":[27,205,209],"scoring":[28],"function":[29,148,216],"estimates":[31],"free":[33,146,214],"energy":[34,147,206,215],"change":[35],"upon":[36],"binding.":[37],"Interestingly,":[38],"this":[39],"applies":[41],"Lamarckian":[43,81,106,131],"model":[44,187],"genetics,":[46],"which":[48],"environmental":[49],"adaptations":[50],"an":[52],"individual's":[53],"phenotype":[54],"are":[55,217],"reverse":[56],"transcribed":[57],"into":[58],"its":[59],"genotype":[60],"become":[62],"heritable":[63],"traits":[64],"(sic).":[65],"We":[66,99],"consider":[67],"three":[68],"search":[69,210],"methods,":[70],"Monte":[71],"Carlo":[72],"simulated":[73,119],"annealing,":[74],"traditional":[76,104],"genetic":[77,82,107,132],"algorithm,":[78,83],"compare":[85],"their":[86],"performance":[87],"dockings":[89],"seven":[91],"protein\u2013ligand":[92,158],"test":[93],"systems":[94],"having":[95],"known":[96,157],"three-dimensional":[97],"structure.":[98],"show":[100],"both":[102],"algorithms":[108],"can":[109],"handle":[110],"more":[113],"degrees":[114],"freedom":[116],"than":[117],"annealing":[120],"used":[122],"earlier":[124],"versions":[125],"AUTODOCK,":[127,220],"algorithm":[133],"is":[134],"most":[136],"efficient,":[137],"reliable,":[138],"successful":[140],"three.":[143],"The":[144,185,208],"empirical":[145,213],"was":[149,183,201],"calibrated":[150],"using":[151],"set":[153],"30":[155],"structurally":[156],"complexes":[159],"experimentally":[161],"determined":[162],"binding":[163,171],"constants.":[164],"Linear":[165],"regression":[166],"analysis":[167],"observed":[170],"constants":[172],"terms":[174],"wide":[177],"variety":[178],"structure-derived":[180],"molecular":[181],"properties":[182],"performed.":[184],"final":[186],"had":[188],"residual":[190],"standard":[191],"error":[192],"9.11":[194],"kJ":[195],"mol\u22121":[196],"(2.177":[197],"kcal":[198],"mol\u22121)":[199],"chosen":[202],"as":[203],"function.":[207],"methods":[211],"available":[218],"version":[221],"3.0.":[222],"\u00a9":[223],"1998":[224,235],"John":[225],"Wiley":[226],"&":[227],"Sons,":[228],"Inc.":[229],"J":[230],"Comput":[231],"Chem":[232],"19:":[233],"1639\u20131662,":[234]},"counts_by_year":[{"year":2026,"cited_by_count":80},{"year":2025,"cited_by_count":426},{"year":2024,"cited_by_count":480},{"year":2023,"cited_by_count":484},{"year":2022,"cited_by_count":540},{"year":2021,"cited_by_count":551},{"year":2020,"cited_by_count":556},{"year":2019,"cited_by_count":496},{"year":2018,"cited_by_count":492},{"year":2017,"cited_by_count":455},{"year":2016,"cited_by_count":490},{"year":2015,"cited_by_count":445},{"year":2014,"cited_by_count":502},{"year":2013,"cited_by_count":538},{"year":2012,"cited_by_count":595}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}