{"id":"https://openalex.org/W3092528982","doi":"https://doi.org/10.1093/bib/bbaa239","title":"MCCS, a novel characterization method for protein\u2013ligand complex","display_name":"MCCS, a novel characterization method for protein\u2013ligand complex","publication_year":2020,"publication_date":"2020-08-28","ids":{"openalex":"https://openalex.org/W3092528982","doi":"https://doi.org/10.1093/bib/bbaa239","mag":"3092528982","pmid":"https://pubmed.ncbi.nlm.nih.gov/33051641"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa239","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa239","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8293830","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078781198","display_name":"Maozi Chen","orcid":"https://orcid.org/0000-0002-0763-6963"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maozi Chen","raw_affiliation_strings":["University of Pittsburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pittsburgh","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076924374","display_name":"Zhiwei Feng","orcid":"https://orcid.org/0000-0001-6533-8932"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhiwei Feng","raw_affiliation_strings":["University of Pittsburgh"],"raw_orcid":"https://orcid.org/0000-0001-6533-8932","affiliations":[{"raw_affiliation_string":"University of Pittsburgh","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104636404","display_name":"Siyi Wang","orcid":"https://orcid.org/0009-0007-0865-4462"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siyi Wang","raw_affiliation_strings":["University of Pittsburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pittsburgh","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033102800","display_name":"Weiwei Lin","orcid":"https://orcid.org/0000-0001-7040-8413"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weiwei Lin","raw_affiliation_strings":["University of Pittsburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pittsburgh","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028011485","display_name":"Xiang\u2010Qun Xie","orcid":"https://orcid.org/0000-0002-6881-6175"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiang-Qun Xie","raw_affiliation_strings":["University of Pittsburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pittsburgh","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5028011485"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.2432,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.84673913,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9962999820709229,"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":0.9779000282287598,"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/computational-biology","display_name":"Computational biology","score":0.6343263387680054},{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.5679539442062378},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.475331574678421},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.4718741476535797},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.46179887652397156},{"id":"https://openalex.org/keywords/molecular-recognition","display_name":"Molecular recognition","score":0.4540000259876251},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4439542293548584},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.427744060754776},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.37664127349853516},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.35474562644958496},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.348200261592865},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.25152939558029175},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22376379370689392},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.17543914914131165},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15207970142364502},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.10801184177398682}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6343263387680054},{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.5679539442062378},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.475331574678421},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.4718741476535797},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.46179887652397156},{"id":"https://openalex.org/C179303850","wikidata":"https://www.wikidata.org/wiki/Q4300362","display_name":"Molecular recognition","level":3,"score":0.4540000259876251},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4439542293548584},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.427744060754776},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.37664127349853516},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35474562644958496},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.348200261592865},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.25152939558029175},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22376379370689392},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.17543914914131165},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15207970142364502},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.10801184177398682},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","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/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":3,"locations":[{"id":"doi:10.1093/bib/bbaa239","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa239","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33051641","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33051641","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8293830","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8293830","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8293830","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8293830","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":"Brief Bioinform","raw_type":"Text"},"sustainable_development_goals":[{"score":0.8799999952316284,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2408914377","display_name":null,"funder_award_id":"P30 DA035778A1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8631900127","display_name":null,"funder_award_id":"P30 DA035778","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W238301194","https://openalex.org/W1548178570","https://openalex.org/W1592950931","https://openalex.org/W1833104430","https://openalex.org/W1980933072","https://openalex.org/W1983304433","https://openalex.org/W1985588649","https://openalex.org/W1994052145","https://openalex.org/W1995155014","https://openalex.org/W2004595546","https://openalex.org/W2005174659","https://openalex.org/W2011658408","https://openalex.org/W2028629022","https://openalex.org/W2049502419","https://openalex.org/W2049756496","https://openalex.org/W2052030759","https://openalex.org/W2060874643","https://openalex.org/W2064573845","https://openalex.org/W2103300124","https://openalex.org/W2105668062","https://openalex.org/W2115318272","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2134967712","https://openalex.org/W2142868265","https://openalex.org/W2147993766","https://openalex.org/W2166765429","https://openalex.org/W2323104785","https://openalex.org/W2327581403","https://openalex.org/W2330799739","https://openalex.org/W2404280981","https://openalex.org/W2533852048","https://openalex.org/W2754993961","https://openalex.org/W2766694609","https://openalex.org/W2768177014","https://openalex.org/W2786807119","https://openalex.org/W2886541183","https://openalex.org/W2914877211","https://openalex.org/W2918278359","https://openalex.org/W2919203345","https://openalex.org/W2951048875","https://openalex.org/W2954728343","https://openalex.org/W3003713259","https://openalex.org/W4242360498"],"related_works":["https://openalex.org/W2939998722","https://openalex.org/W2169750653","https://openalex.org/W2195592873","https://openalex.org/W1971782741","https://openalex.org/W3005062988","https://openalex.org/W2075777827","https://openalex.org/W4211217675","https://openalex.org/W2592466923","https://openalex.org/W1555254413","https://openalex.org/W4231759675"],"abstract_inverted_index":{"Delineating":[0],"the":[1,11,19,79,87,94,116,121,124,133,140,168,172],"fingerprint":[2],"or":[3,52],"feature":[4,81],"vector":[5,114,143],"of":[6,24,45,82,97,106,123],"a":[7,68,113,128,157,163],"receptor/protein":[8],"will":[9],"facilitate":[10],"structural":[12],"and":[13,22,29,130,151,174],"biological":[14],"studies,":[15],"as":[16,18],"well":[17],"rational":[20],"design":[21],"development":[23],"drugs":[25],"with":[26,136],"high":[27],"affinities":[28],"selectivity.":[30],"However,":[31],"protein":[32,47,169],"is":[33,144,182],"complicated":[34],"by":[35],"its":[36,46],"different":[37],"functional":[38],"regions":[39],"that":[40],"can":[41],"bind":[42],"to":[43,76,119,160],"some":[44],"partner(s),":[48],"substrate(s),":[49],"orthosteric":[50],"ligand(s)":[51],"allosteric":[53],"modulator(s)":[54],"where":[55,179],"cogent":[56],"methods":[57],"like":[58],"molecular":[59,180],"fingerprints":[60],"do":[61],"not":[62],"work":[63,155],"well.":[64],"We":[65,110],"here":[66],"elaborate":[67],"scoring-function-based":[69],"computing":[70],"protocol":[71],"Molecular":[72],"Complex":[73],"Characterizing":[74],"System":[75],"help":[77],"characterize":[78],"binding":[80],"protein-ligand":[83],"complexes.":[84],"Based":[85],"on":[86],"reported":[88],"receptor-ligand":[89],"interactions,":[90],"we":[91],"first":[92],"quantitate":[93],"energy":[95,108,117,141],"contribution":[96,118,142],"each":[98],"individual":[99],"residue":[100],"which":[101],"may":[102],"be":[103],"an":[104,175],"alternative":[105],"MD-based":[107],"decomposition.":[109],"then":[111],"construct":[112],"for":[115,146,166],"represent":[120],"pattern":[122],"ligand":[125],"recognition":[126],"at":[127],"receptor":[129],"qualitatively":[131],"analyze":[132],"matching":[134],"level":[135],"other":[137],"receptors.":[138],"Finally,":[139],"explored":[145],"extensive":[147],"use":[148],"in":[149,171],"similarity":[150],"clustering.":[152],"The":[153],"present":[154],"provides":[156],"new":[158],"approach":[159],"cluster":[161],"proteins,":[162],"perspective":[164],"counterpart":[165],"determining":[167],"characteristics":[170],"binding,":[173],"advanced":[176],"screening":[177],"technique":[178],"docking":[181],"applicable.":[183]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
