{"id":"https://openalex.org/W4403681209","doi":"https://doi.org/10.4310/cis.241021221101","title":"Docking strategies for predicting protein-ligand interactions and their application to structure-based drug design","display_name":"Docking strategies for predicting protein-ligand interactions and their application to structure-based drug design","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4403681209","doi":"https://doi.org/10.4310/cis.241021221101","pmid":"https://pubmed.ncbi.nlm.nih.gov/39584017"},"language":"en","primary_location":{"id":"doi:10.4310/cis.241021221101","is_oa":false,"landing_page_url":"https://doi.org/10.4310/cis.241021221101","pdf_url":null,"source":{"id":"https://openalex.org/S2765060502","display_name":"Communications in Information and Systems","issn_l":"1526-7555","issn":["1526-7555","2163-4548"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Communications in Information and Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11583305/pdf/nihms-1993634.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101650425","display_name":"Zhiwei Ma","orcid":"https://orcid.org/0000-0001-9243-2211"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhiwei Ma","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri-Columbia, USA","Dalton Cardiovascular Research Center, University of Missouri-Columbia USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri-Columbia, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri-Columbia USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046618745","display_name":"Abeeb Ajibade","orcid":null},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abeeb Ajibade","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri-Columbia; Department of Physics and Astronomy, University of Missouri-Columbia, USA","Dalton Cardiovascular Research Center, University of Missouri-Columbia","Department of Physics and Astronomy, University of Missouri-Columbia USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri-Columbia; Department of Physics and Astronomy, University of Missouri-Columbia, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri-Columbia","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Physics and Astronomy, University of Missouri-Columbia USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081082371","display_name":"Xiaoqin Zou","orcid":"https://orcid.org/0000-0003-0637-8648"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoqin Zou","raw_affiliation_strings":["Dalton Cardiovascular Research Center, University of Missouri-Columbia, Department of Physics and Astronomy; University of Missouri-Columbia, Department of Biochemistry, University of Missouri-Columbia; Institute for Data Science and Informatics, University of Missouri-Columbia, USA","Institute for Data Science and Informatics, University of Missouri-Columbia USA","Department of Biochemistry, University of Missouri-Columbia","Department of Physics and Astronomy, University of Missouri-Columbia","Dalton Cardiovascular Research Center, University of Missouri-Columbia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri-Columbia, Department of Physics and Astronomy; University of Missouri-Columbia, Department of Biochemistry, University of Missouri-Columbia; Institute for Data Science and Informatics, University of Missouri-Columbia, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Institute for Data Science and Informatics, University of Missouri-Columbia USA","institution_ids":[]},{"raw_affiliation_string":"Department of Biochemistry, University of Missouri-Columbia","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Physics and Astronomy, University of Missouri-Columbia","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dalton Cardiovascular Research Center, University of Missouri-Columbia","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101650425"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":3.937,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.94505254,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"3","first_page":"199","last_page":"230"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.996999979019165,"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":0.996999979019165,"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/docking","display_name":"Docking (animal)","score":0.6105389595031738},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.5780202150344849},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5114321112632751},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4851763844490051},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.44579246640205383},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.36513739824295044},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3508734703063965},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.34194034337997437},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.3383234739303589},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.23440852761268616},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.205025315284729},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.18855515122413635},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1681230068206787},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14079603552818298},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.12374284863471985}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6105389595031738},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.5780202150344849},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5114321112632751},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4851763844490051},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.44579246640205383},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.36513739824295044},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3508734703063965},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.34194034337997437},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.3383234739303589},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.23440852761268616},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.205025315284729},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.18855515122413635},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1681230068206787},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14079603552818298},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.12374284863471985},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.4310/cis.241021221101","is_oa":false,"landing_page_url":"https://doi.org/10.4310/cis.241021221101","pdf_url":null,"source":{"id":"https://openalex.org/S2765060502","display_name":"Communications in Information and Systems","issn_l":"1526-7555","issn":["1526-7555","2163-4548"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Communications in Information and Systems","raw_type":"journal-article"},{"id":"pmid:39584017","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39584017","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":"Communications in information and systems","raw_type":null},{"id":"pmh:oai:europepmc.org:11343644","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11583305","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11583305/pdf/nihms-1993634.pdf","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11583305","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11583305/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Commun Inf Syst","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:11343644","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11583305","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11583305/pdf/nihms-1993634.pdf","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4156299872","display_name":null,"funder_award_id":"R35GM136409","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5089104101","display_name":null,"funder_award_id":"R01HL126774","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4403681209.pdf"},"referenced_works_count":127,"referenced_works":["https://openalex.org/W1653739410","https://openalex.org/W1950993160","https://openalex.org/W1966041739","https://openalex.org/W1968682237","https://openalex.org/W1984021058","https://openalex.org/W1985588649","https://openalex.org/W1986240377","https://openalex.org/W1987012451","https://openalex.org/W2000864931","https://openalex.org/W2002733813","https://openalex.org/W2003356525","https://openalex.org/W2010004274","https://openalex.org/W2010286440","https://openalex.org/W2012084558","https://openalex.org/W2013085020","https://openalex.org/W2013848575","https://openalex.org/W2014952106","https://openalex.org/W2015517515","https://openalex.org/W2025556412","https://openalex.org/W2027408247","https://openalex.org/W2030286884","https://openalex.org/W2033882981","https://openalex.org/W2040990879","https://openalex.org/W2042572511","https://openalex.org/W2043629638","https://openalex.org/W2046891749","https://openalex.org/W2048513282","https://openalex.org/W2050456292","https://openalex.org/W2053174787","https://openalex.org/W2053717624","https://openalex.org/W2061745280","https://openalex.org/W2061750520","https://openalex.org/W2064505617","https://openalex.org/W2066962978","https://openalex.org/W2067455153","https://openalex.org/W2072180710","https://openalex.org/W2078374001","https://openalex.org/W2080653934","https://openalex.org/W2090431249","https://openalex.org/W2092541287","https://openalex.org/W2093221728","https://openalex.org/W2093313511","https://openalex.org/W2095750235","https://openalex.org/W2096929343","https://openalex.org/W2098971704","https://openalex.org/W2105527266","https://openalex.org/W2108257090","https://openalex.org/W2109476464","https://openalex.org/W2109622527","https://openalex.org/W2112276613","https://openalex.org/W2113030357","https://openalex.org/W2114162221","https://openalex.org/W2114779636","https://openalex.org/W2123529526","https://openalex.org/W2124751168","https://openalex.org/W2125200271","https://openalex.org/W2128332459","https://openalex.org/W2134967712","https://openalex.org/W2138512826","https://openalex.org/W2145682943","https://openalex.org/W2148512505","https://openalex.org/W2152630148","https://openalex.org/W2154492420","https://openalex.org/W2162027701","https://openalex.org/W2165533187","https://openalex.org/W2169562071","https://openalex.org/W2170146596","https://openalex.org/W2183050958","https://openalex.org/W2200866600","https://openalex.org/W2220335167","https://openalex.org/W2231215589","https://openalex.org/W2266013672","https://openalex.org/W2311607323","https://openalex.org/W2364255377","https://openalex.org/W2388080941","https://openalex.org/W2408522200","https://openalex.org/W2467739699","https://openalex.org/W2498179566","https://openalex.org/W2527541313","https://openalex.org/W2550887636","https://openalex.org/W2558999090","https://openalex.org/W2608559058","https://openalex.org/W2643648096","https://openalex.org/W2702177082","https://openalex.org/W2727656886","https://openalex.org/W2747134193","https://openalex.org/W2751445595","https://openalex.org/W2762358889","https://openalex.org/W2774371249","https://openalex.org/W2774738748","https://openalex.org/W2781821160","https://openalex.org/W2784213390","https://openalex.org/W2790808809","https://openalex.org/W2793534579","https://openalex.org/W2801991413","https://openalex.org/W2802492120","https://openalex.org/W2887039457","https://openalex.org/W2910318997","https://openalex.org/W2912315505","https://openalex.org/W2922063386","https://openalex.org/W2937307539","https://openalex.org/W2949867299","https://openalex.org/W2955998834","https://openalex.org/W2982145277","https://openalex.org/W3001433048","https://openalex.org/W3002058234","https://openalex.org/W3008726875","https://openalex.org/W3030018498","https://openalex.org/W3043660595","https://openalex.org/W3080588469","https://openalex.org/W3112376646","https://openalex.org/W3135576859","https://openalex.org/W3138987436","https://openalex.org/W3177828909","https://openalex.org/W3206666534","https://openalex.org/W3211414347","https://openalex.org/W3211795435","https://openalex.org/W4210716706","https://openalex.org/W4239761798","https://openalex.org/W4280538744","https://openalex.org/W4289518623","https://openalex.org/W4293799446","https://openalex.org/W4322832229","https://openalex.org/W4379600614","https://openalex.org/W4388034457","https://openalex.org/W4388615774","https://openalex.org/W4391542588"],"related_works":["https://openalex.org/W1581147483","https://openalex.org/W4310018788","https://openalex.org/W4398796548","https://openalex.org/W2329052364","https://openalex.org/W2162967120","https://openalex.org/W1567411871","https://openalex.org/W2553094381","https://openalex.org/W2072180710","https://openalex.org/W2794807012","https://openalex.org/W2301625241"],"abstract_inverted_index":{"Molecular":[0],"docking":[1,50,120,144,153],"stands":[2],"as":[3,111],"a":[4,44],"pivotal":[5],"element":[6],"in":[7,19,72,90,134,145],"the":[8,30,48,54,61,74,81,85,91,105,128,141],"realm":[9],"of":[10,64,77,87,93,108,119,131,143],"computer-aided":[11],"drug":[12,102,112],"design":[13],"(CADD),":[14],"consistently":[15],"contributing":[16],"to":[17,28,37],"advancements":[18],"pharmaceutical":[20],"research.":[21],"In":[22],"essence,":[23],"it":[24],"employs":[25],"computer":[26],"algorithms":[27],"identify":[29],"\"best\"":[31],"match":[32],"between":[33],"two":[34,65],"molecules,":[35],"akin":[36],"solving":[38],"intricate":[39],"three-dimensional":[40],"jigsaw":[41],"puzzles.":[42],"At":[43],"more":[45],"stringent":[46],"level,":[47],"molecular":[49,132],"challenge":[51],"entails":[52],"predicting":[53],"accurate":[55],"bound":[56],"association":[57],"state":[58],"based":[59],"on":[60],"atomic":[62,82],"coordinates":[63],"molecules.":[66],"This":[67,114],"process":[68],"assumes":[69],"particular":[70],"significance":[71],"unraveling":[73],"mechanistic":[75],"intricacies":[76],"physicochemical":[78,129],"interactions":[79],"at":[80],"scale.":[83],"Notably,":[84],"application":[86],"docking,":[88],"especially":[89],"context":[92],"protein-small":[94],"molecule":[95],"interactions,":[96,136],"holds":[97],"wide-ranging":[98],"implications":[99],"for":[100],"structure-based":[101],"design,":[103],"given":[104],"prevalent":[106],"use":[107],"small":[109],"compounds":[110],"candidates.":[113],"study":[115],"provides":[116],"an":[117],"overview":[118],"methodologies,":[121],"delves":[122],"into":[123],"recent":[124],"key":[125],"developments,":[126],"elucidates":[127],"underpinnings":[130],"recognition":[133],"protein-ligand":[135],"and":[137],"concludes":[138],"by":[139],"addressing":[140],"applications":[142],"virtual":[146],"screening,":[147],"alongside":[148],"current":[149],"challenges":[150],"within":[151],"existing":[152],"methods.":[154]},"counts_by_year":[{"year":2026,"cited_by_count":12}],"updated_date":"2026-05-29T09:21:14.243279","created_date":"2025-10-10T00:00:00"}
