{"id":"https://openalex.org/W3036774570","doi":"https://doi.org/10.1109/tcbb.2020.3002776","title":"On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions","display_name":"On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions","publication_year":2020,"publication_date":"2020-06-16","ids":{"openalex":"https://openalex.org/W3036774570","doi":"https://doi.org/10.1109/tcbb.2020.3002776","mag":"3036774570","pmid":"https://pubmed.ncbi.nlm.nih.gov/32750865"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.3002776","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3002776","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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/A5074973688","display_name":"Yajun Dai","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yajun Dai","raw_affiliation_strings":["School of Mathematical Sciences, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101621563","display_name":"Yang Li","orcid":"https://orcid.org/0000-0001-7304-3851"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Li","raw_affiliation_strings":["College of Life Sciences, Nankai University, Tianjin, China","School of Mathematical Sciences, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Sciences, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"School of Mathematical Sciences, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100402258","display_name":"Liping Wang","orcid":"https://orcid.org/0000-0002-5526-0868"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liping Wang","raw_affiliation_strings":["School of Mathematical Sciences, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020435329","display_name":"Zhenling Peng","orcid":"https://orcid.org/0000-0003-0303-6693"},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenling Peng","raw_affiliation_strings":["Center for Applied Mathematics, Tianjin University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Applied Mathematics, Tianjin University, Tianjin, China","institution_ids":["https://openalex.org/I162868743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107636936","display_name":"Jianyi Yang","orcid":"https://orcid.org/0000-0003-2912-7737"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianyi Yang","raw_affiliation_strings":["School of Mathematical Sciences, Nankai University, Tianjin, China"],"raw_orcid":"https://orcid.org/0000-0003-2912-7737","affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5074973688"],"corresponding_institution_ids":["https://openalex.org/I205237279"],"apc_list":null,"apc_paid":null,"fwci":0.1445,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5218562,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"19","issue":"1","first_page":"569","last_page":"574"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9977999925613403,"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":0.994700014591217,"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":0.7527914047241211},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6982388496398926},{"id":"https://openalex.org/keywords/monomer","display_name":"Monomer","score":0.6703073978424072},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6495124101638794},{"id":"https://openalex.org/keywords/protein-quaternary-structure","display_name":"Protein quaternary structure","score":0.5993752479553223},{"id":"https://openalex.org/keywords/searching-the-conformational-space-for-docking","display_name":"Searching the conformational space for docking","score":0.5421863198280334},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.5222681164741516},{"id":"https://openalex.org/keywords/molecular-model","display_name":"Molecular model","score":0.4844101071357727},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.4742357134819031},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.473770409822464},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4623172879219055},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.4232540726661682},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.41134893894195557},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3742808997631073},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.18896549940109253},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.0982036292552948},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.07742971181869507},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.06372624635696411},{"id":"https://openalex.org/keywords/polymer","display_name":"Polymer","score":0.05224204063415527}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7527914047241211},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6982388496398926},{"id":"https://openalex.org/C166940927","wikidata":"https://www.wikidata.org/wiki/Q178827","display_name":"Monomer","level":3,"score":0.6703073978424072},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6495124101638794},{"id":"https://openalex.org/C7927669","wikidata":"https://www.wikidata.org/wiki/Q898529","display_name":"Protein quaternary structure","level":4,"score":0.5993752479553223},{"id":"https://openalex.org/C44695244","wikidata":"https://www.wikidata.org/wiki/Q7441727","display_name":"Searching the conformational space for docking","level":3,"score":0.5421863198280334},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.5222681164741516},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.4844101071357727},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.4742357134819031},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.473770409822464},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4623172879219055},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4232540726661682},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.41134893894195557},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3742808997631073},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.18896549940109253},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0982036292552948},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.07742971181869507},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.06372624635696411},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.05224204063415527},{"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/C104292427","wikidata":"https://www.wikidata.org/wiki/Q899781","display_name":"Protein subunit","level":3,"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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:10.1109/tcbb.2020.3002776","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3002776","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32750865","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32750865","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8799999952316284,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G6339323267","display_name":null,"funder_award_id":"11871290","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G649404935","display_name":null,"funder_award_id":"61873185","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8532275144","display_name":null,"funder_award_id":"161003","funder_id":"https://openalex.org/F4320334945","funder_display_name":"Fok Ying Tong Education Foundation"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320334945","display_name":"Fok Ying Tong Education Foundation","ror":"https://ror.org/01mv9t934"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1971248251","https://openalex.org/W1998568556","https://openalex.org/W2018661561","https://openalex.org/W2035503835","https://openalex.org/W2042572511","https://openalex.org/W2054310317","https://openalex.org/W2072180710","https://openalex.org/W2090649877","https://openalex.org/W2092285329","https://openalex.org/W2096360825","https://openalex.org/W2104812418","https://openalex.org/W2105527266","https://openalex.org/W2107624662","https://openalex.org/W2128332459","https://openalex.org/W2134967712","https://openalex.org/W2140538197","https://openalex.org/W2144258433","https://openalex.org/W2146233784","https://openalex.org/W2152299045","https://openalex.org/W2158660006","https://openalex.org/W2158964183","https://openalex.org/W2334483166","https://openalex.org/W2544136853","https://openalex.org/W2600971009","https://openalex.org/W2768330140","https://openalex.org/W2790133599","https://openalex.org/W2795016431","https://openalex.org/W2800648160","https://openalex.org/W2937705502","https://openalex.org/W2960291854","https://openalex.org/W2979876181"],"related_works":["https://openalex.org/W2152236566","https://openalex.org/W2078959398","https://openalex.org/W2775216884","https://openalex.org/W2885308902","https://openalex.org/W2031553931","https://openalex.org/W2331956508","https://openalex.org/W3105771019","https://openalex.org/W2058311929","https://openalex.org/W2085043181","https://openalex.org/W2135472700"],"abstract_inverted_index":{"Many":[0],"ligands":[1,88],"simultaneously":[2],"interact":[3],"with":[4,102,129,134,142],"multiple":[5,90,103],"protein":[6],"chains":[7,91,104],"in":[8,74,92,106,172],"quaternary":[9],"structure":[10,29],"(QS).":[11],"However,":[12],"a":[13,67],"significant":[14],"number":[15],"of":[16,22,40,70,77,167],"previous":[17],"studies":[18,174],"on":[19,27,56,158,175],"template-based":[20],"modeling":[21],"protein-ligand":[23,72,176],"interactions":[24,73],"were":[25,153],"based":[26,55],"monomeric":[28],"(MS),":[30],"which":[31],"may":[32],"suffer":[33],"from":[34],"incomplete":[35],"binding":[36,61,110,131],"information.":[37],"The":[38],"defects":[39],"using":[41],"MS":[42,121,171],"rather":[43,169],"than":[44,98,119,141,170],"QS":[45,93,117,135,168],"have":[46],"not":[47],"been":[48],"systematically":[49],"studied":[50],"before.":[51],"In":[52],"this":[53,159],"work,":[54,160],"molecular":[57],"docking":[58,133,151],"experiments":[59],"and":[60],"free":[62,111],"energy":[63,112],"estimations,":[64],"we":[65],"performed":[66],"large-scale":[68],"comparison":[69],"the":[71,107,109,116,120],"both":[75],"forms":[76],"structures.":[78],"We":[79],"found":[80],"that":[81],"1)":[82],"about":[83,146],"18.6":[84],"percent":[85,100,127,148],"biologically":[86],"relevant":[87],"bind":[89],"simultaneously.":[94],"2)":[95],"For":[96,124],"more":[97,137],"95":[99],"complexes":[101,128],"involved":[105],"interactions,":[108],"is":[113,162],"lower":[114],"for":[115,145],"form":[118],"form.":[122],"3)":[123],"over":[125],"70":[126],"multi-chain":[130],"pockets,":[132],"yields":[136],"accurate":[138,150],"ligand":[139],"conformations":[140,152],"MS.":[143,156],"While":[144],"1.82":[147],"complexes,":[149],"obtained":[154],"by":[155],"Based":[157],"it":[161],"encouraged":[163],"to":[164],"make":[165],"use":[166],"future":[173],"interactions.":[177]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
