{"id":"https://openalex.org/W4324129241","doi":"https://doi.org/10.1021/acs.jcim.2c01436","title":"Deep Learning Model for Efficient Protein\u2013Ligand Docking with Implicit Side-Chain Flexibility","display_name":"Deep Learning Model for Efficient Protein\u2013Ligand Docking with Implicit Side-Chain Flexibility","publication_year":2023,"publication_date":"2023-03-14","ids":{"openalex":"https://openalex.org/W4324129241","doi":"https://doi.org/10.1021/acs.jcim.2c01436","pmid":"https://pubmed.ncbi.nlm.nih.gov/36916514"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01436","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01436","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/A5029888767","display_name":"Matthew R. Masters","orcid":null},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Matthew R. Masters","raw_affiliation_strings":["Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101138262","display_name":"Amr H. Mahmoud","orcid":null},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Amr H. Mahmoud","raw_affiliation_strings":["Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100643676","display_name":"Wei Yao","orcid":"https://orcid.org/0009-0009-4005-4410"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Yao Wei","raw_affiliation_strings":["Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041891399","display_name":"Markus A. Lill","orcid":null},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Markus A. Lill","raw_affiliation_strings":["Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-3023-5188","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5041891399"],"corresponding_institution_ids":["https://openalex.org/I1850255"],"apc_list":null,"apc_paid":null,"fwci":10.7588,"has_fulltext":false,"cited_by_count":58,"citation_normalized_percentile":{"value":0.98724863,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"63","issue":"6","first_page":"1695","last_page":"1707"},"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":0.996999979019165,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9948999881744385,"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/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.8846843242645264},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.793386697769165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6443192958831787},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5929232835769653},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5189040303230286},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46537989377975464},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.43037599325180054},{"id":"https://openalex.org/keywords/target-protein","display_name":"Target protein","score":0.4253210723400116},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3891522288322449},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2507885992527008},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22805523872375488},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11699965596199036},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08266839385032654}],"concepts":[{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.8846843242645264},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.793386697769165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6443192958831787},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5929232835769653},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5189040303230286},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46537989377975464},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.43037599325180054},{"id":"https://openalex.org/C2780430158","wikidata":"https://www.wikidata.org/wiki/Q7685902","display_name":"Target protein","level":3,"score":0.4253210723400116},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3891522288322449},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2507885992527008},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22805523872375488},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11699965596199036},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08266839385032654},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D008024","descriptor_name":"Ligands","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c01436","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01436","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:36916514","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36916514","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":[],"awards":[{"id":"https://openalex.org/G2639422791","display_name":null,"funder_award_id":"310030_197629","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1856811566","https://openalex.org/W2001816314","https://openalex.org/W2010004274","https://openalex.org/W2017422910","https://openalex.org/W2018661561","https://openalex.org/W2019471147","https://openalex.org/W2028629022","https://openalex.org/W2033206800","https://openalex.org/W2039526577","https://openalex.org/W2041668538","https://openalex.org/W2064922889","https://openalex.org/W2086642544","https://openalex.org/W2095172966","https://openalex.org/W2118226640","https://openalex.org/W2145356148","https://openalex.org/W2147993766","https://openalex.org/W2151971404","https://openalex.org/W2152630148","https://openalex.org/W2244785476","https://openalex.org/W2404280981","https://openalex.org/W2464107291","https://openalex.org/W2526925775","https://openalex.org/W2527189750","https://openalex.org/W2541404351","https://openalex.org/W2578119541","https://openalex.org/W2583907533","https://openalex.org/W2594183968","https://openalex.org/W2778051509","https://openalex.org/W2784213390","https://openalex.org/W2803094965","https://openalex.org/W2809216727","https://openalex.org/W2898280479","https://openalex.org/W2902812092","https://openalex.org/W2943893168","https://openalex.org/W2964206522","https://openalex.org/W2974531988","https://openalex.org/W2985816842","https://openalex.org/W2988055229","https://openalex.org/W3005776600","https://openalex.org/W3015572666","https://openalex.org/W3048540906","https://openalex.org/W3098189759","https://openalex.org/W3104508774","https://openalex.org/W3104644561","https://openalex.org/W3113616921","https://openalex.org/W3125542198","https://openalex.org/W3132180101","https://openalex.org/W3146944767","https://openalex.org/W3164107346","https://openalex.org/W3168430821","https://openalex.org/W3171159608","https://openalex.org/W3177828909","https://openalex.org/W3185456481","https://openalex.org/W3195820203","https://openalex.org/W3202227570","https://openalex.org/W4206563428","https://openalex.org/W4220695049","https://openalex.org/W4229459076","https://openalex.org/W4281701642","https://openalex.org/W4285589483"],"related_works":["https://openalex.org/W2057846043","https://openalex.org/W2336040088","https://openalex.org/W2027065525","https://openalex.org/W2750247885","https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2093426296","https://openalex.org/W2005817231","https://openalex.org/W3135576859","https://openalex.org/W2078959398"],"abstract_inverted_index":{"Protein-ligand":[0],"docking":[1,24,60,84,141],"is":[2,50],"an":[3,34,51,90],"essential":[4,52],"tool":[5],"in":[6],"structure-based":[7],"drug":[8,44,68],"design":[9,45],"with":[10],"applications":[11],"ranging":[12],"from":[13],"virtual":[14],"high-throughput":[15],"screening":[16],"to":[17,33,66],"pose":[18,27],"prediction":[19,28,88],"for":[20,26,31,81,129],"lead":[21],"optimization.":[22],"Most":[23],"programs":[25],"are":[29],"optimized":[30],"redocking":[32],"existing":[35],"cocrystallized":[36],"protein":[37,40,48,134],"structure,":[38],"ignoring":[39],"flexibility.":[41],"In":[42],"real-world":[43],"applications,":[46],"however,":[47],"flexibility":[49],"feature":[53],"of":[54,89,100,114,133],"the":[55,87,97],"ligand-binding":[56],"process.":[57],"Flexible":[58],"protein-ligand":[59,83,115],"still":[61],"remains":[62],"a":[63,76,110,130],"significant":[64],"challenge":[65],"computational":[67],"design.":[69],"To":[70],"target":[71],"this":[72],"challenge,":[73],"we":[74],"present":[75],"deep":[77],"learning":[78],"(DL)":[79],"model":[80,106,124],"flexible":[82],"based":[85],"on":[86,109,119],"intermolecular":[91],"Euclidean":[92],"distance":[93],"matrix":[94],"(EDM),":[95],"making":[96],"typical":[98],"use":[99],"iterative":[101],"search":[102],"algorithms":[103],"obsolete.":[104],"The":[105],"was":[107],"trained":[108],"large-scale":[111],"data":[112],"set":[113,132],"complexes":[116],"and":[117,135,138],"evaluated":[118],"independent":[120],"test":[121],"sets.":[122],"Our":[123],"generates":[125],"high":[126],"quality":[127],"poses":[128],"diverse":[131],"ligand":[136],"structures":[137],"outperforms":[139],"comparable":[140],"methods.":[142]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":27},{"year":2023,"cited_by_count":10}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}
