{"id":"https://openalex.org/W2007054671","doi":"https://doi.org/10.1021/ci400729j","title":"Ensemble-Based Docking Using Biased Molecular Dynamics","display_name":"Ensemble-Based Docking Using Biased Molecular Dynamics","publication_year":2014,"publication_date":"2014-06-01","ids":{"openalex":"https://openalex.org/W2007054671","doi":"https://doi.org/10.1021/ci400729j","mag":"2007054671","pmid":"https://pubmed.ncbi.nlm.nih.gov/24881672"},"language":"en","primary_location":{"id":"doi:10.1021/ci400729j","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400729j","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/A5011466708","display_name":"Arthur J. Campbell","orcid":"https://orcid.org/0000-0003-3857-9727"},"institutions":[{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Arthur J. Campbell","raw_affiliation_strings":["AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States","AstraZeneca , R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States"],"affiliations":[{"raw_affiliation_string":"AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States","institution_ids":["https://openalex.org/I4210150756"]},{"raw_affiliation_string":"AstraZeneca , R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083435506","display_name":"Michelle L. Lamb","orcid":"https://orcid.org/0000-0002-3005-8065"},"institutions":[{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michelle L. Lamb","raw_affiliation_strings":["AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States","AstraZeneca , R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States"],"affiliations":[{"raw_affiliation_string":"AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States","institution_ids":["https://openalex.org/I4210150756"]},{"raw_affiliation_string":"AstraZeneca , R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066868698","display_name":"Diane Joseph\u2010McCarthy","orcid":"https://orcid.org/0000-0001-9685-6177"},"institutions":[{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Diane Joseph-McCarthy","raw_affiliation_strings":["AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States","AstraZeneca , R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States"],"affiliations":[{"raw_affiliation_string":"AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States","institution_ids":["https://openalex.org/I4210150756"]},{"raw_affiliation_string":"AstraZeneca , R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5011466708"],"corresponding_institution_ids":["https://openalex.org/I4210150756"],"apc_list":null,"apc_paid":null,"fwci":8.8327,"has_fulltext":false,"cited_by_count":65,"citation_normalized_percentile":{"value":0.98199787,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"54","issue":"7","first_page":"2127","last_page":"2138"},"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":0.9998000264167786,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7929655313491821},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.772574245929718},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7225394248962402},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5026404857635498},{"id":"https://openalex.org/keywords/searching-the-conformational-space-for-docking","display_name":"Searching the conformational space for docking","score":0.49698522686958313},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.4783156216144562},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.46466055512428284},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.44581037759780884},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4275309443473816},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.42505955696105957},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4148104190826416},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.40039077401161194},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.37463921308517456},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3356199860572815},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2996037006378174},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11372357606887817},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07754385471343994}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7929655313491821},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.772574245929718},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7225394248962402},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5026404857635498},{"id":"https://openalex.org/C44695244","wikidata":"https://www.wikidata.org/wiki/Q7441727","display_name":"Searching the conformational space for docking","level":3,"score":0.49698522686958313},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.4783156216144562},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.46466055512428284},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.44581037759780884},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4275309443473816},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.42505955696105957},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4148104190826416},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.40039077401161194},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.37463921308517456},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3356199860572815},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2996037006378174},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11372357606887817},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07754385471343994},{"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}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051357","descriptor_name":"Cyclin-Dependent Kinase 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci400729j","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400729j","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:24881672","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24881672","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":0.6700000166893005,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W123043565","https://openalex.org/W1531401772","https://openalex.org/W1969875513","https://openalex.org/W1972148009","https://openalex.org/W1975570414","https://openalex.org/W1975691556","https://openalex.org/W1976499671","https://openalex.org/W1977173978","https://openalex.org/W1978159078","https://openalex.org/W1978880915","https://openalex.org/W1982441109","https://openalex.org/W1985407614","https://openalex.org/W1985588649","https://openalex.org/W1989814214","https://openalex.org/W1993403967","https://openalex.org/W1993804731","https://openalex.org/W1999805037","https://openalex.org/W2008258090","https://openalex.org/W2008518939","https://openalex.org/W2009423060","https://openalex.org/W2011616792","https://openalex.org/W2028134326","https://openalex.org/W2028263411","https://openalex.org/W2030423316","https://openalex.org/W2037535298","https://openalex.org/W2041046009","https://openalex.org/W2057846043","https://openalex.org/W2058479011","https://openalex.org/W2060754823","https://openalex.org/W2063083610","https://openalex.org/W2066123607","https://openalex.org/W2067174909","https://openalex.org/W2072683434","https://openalex.org/W2075802963","https://openalex.org/W2079153029","https://openalex.org/W2079199763","https://openalex.org/W2080590432","https://openalex.org/W2097029677","https://openalex.org/W2099211347","https://openalex.org/W2106140689","https://openalex.org/W2120686999","https://openalex.org/W2121895929","https://openalex.org/W2144288821","https://openalex.org/W2147993766","https://openalex.org/W2150981663","https://openalex.org/W2153228625","https://openalex.org/W2161134038","https://openalex.org/W2163915395","https://openalex.org/W2174570645"],"related_works":["https://openalex.org/W1992786240","https://openalex.org/W2057846043","https://openalex.org/W2100241209","https://openalex.org/W2336040088","https://openalex.org/W2013760445","https://openalex.org/W2106810308","https://openalex.org/W1974879154","https://openalex.org/W2089879448","https://openalex.org/W3004756300","https://openalex.org/W2007054671"],"abstract_inverted_index":{"Proteins":[0],"are":[1,77,122,156,168,199],"dynamic":[2],"molecules,":[3],"and":[4,15,141,166,180,201,210],"understanding":[5],"their":[6],"movements,":[7],"especially":[8],"as":[9,47,49],"they":[10],"relate":[11],"to":[12,22,38,56,66,79,93,114,158,170,177],"molecular":[13],"recognition":[14],"protein-ligand":[16,127],"interactions,":[17],"poses":[18],"a":[19,107,160],"significant":[20],"challenge":[21],"structure-based":[23],"drug":[24,35],"discovery.":[25],"In":[26],"most":[27],"instances,":[28],"protein":[29,84,98,164],"flexibility":[30,58],"is":[31,70,204],"underrepresented":[32],"in":[33,59],"computer-aided":[34],"design":[36],"due":[37],"uncertainties":[39],"on":[40],"how":[41],"it":[42],"should":[43],"be":[44,91],"accurately":[45],"modeled":[46],"well":[48],"the":[50,60,95,101,116,136,146,152,183,191,202],"computational":[51],"cost":[52],"associated":[53],"with":[54],"attempting":[55],"incorporate":[57],"calculations.":[61],"One":[62],"approach":[63,109],"that":[64,110,171],"aims":[65],"address":[67],"these":[68],"issues":[69],"ensemble-based":[71],"docking.":[72,103],"With":[73],"this":[74,178],"technique,":[75],"ligands":[76,167],"docked":[78,169],"an":[80,125],"ensemble":[81,96,179],"of":[82,97,135,145,151,163,174,190,197],"rigid":[83],"conformations.":[85,175],"Molecular":[86],"dynamics":[87],"(MD)":[88],"simulations":[89,113,121],"can":[90],"used":[92],"generate":[94,115],"conformations":[99],"for":[100,206],"subsequent":[102],"Here":[104],"we":[105],"present":[106],"novel":[108],"uses":[111],"biased-MD":[112],"docking":[117],"ensemble.":[118],"The":[119,131],"MD":[120],"biased":[123],"toward":[124],"initial":[126],"X-ray":[128],"complex":[129],"structure.":[130],"biasing":[132,198],"maintains":[133],"some":[134],"original":[137],"crystallographic":[138],"pocket-ligand":[139],"information":[140],"thereby":[142],"enhances":[143],"sampling":[144],"more":[147],"relevant":[148],"conformational":[149],"space":[150],"protein.":[153],"Resulting":[154],"trajectories":[155],"clustered":[157],"select":[159],"representative":[161],"set":[162,173],"conformations,":[165],"reduced":[172],"Cross-docking":[176],"then":[181],"selecting":[182],"lowest":[184],"scoring":[185],"pose":[186],"enables":[187],"reliable":[188],"identification":[189],"correct":[192],"binding":[193],"mode.":[194],"Various":[195],"levels":[196],"investigated,":[200],"method":[203],"validated":[205],"cyclin-dependent":[207],"kinase":[208],"2":[209],"factor":[211],"Xa.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":4}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2025-10-10T00:00:00"}
