{"id":"https://openalex.org/W3209435597","doi":"https://doi.org/10.1093/bioinformatics/btab762","title":"CSM-AB: graph-based antibody\u2013antigen binding affinity prediction and docking scoring function","display_name":"CSM-AB: graph-based antibody\u2013antigen binding affinity prediction and docking scoring function","publication_year":2021,"publication_date":"2021-11-01","ids":{"openalex":"https://openalex.org/W3209435597","doi":"https://doi.org/10.1093/bioinformatics/btab762","mag":"3209435597","pmid":"https://pubmed.ncbi.nlm.nih.gov/34734992"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab762","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab762","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5076251011","display_name":"Yoochan Myung","orcid":"https://orcid.org/0000-0002-6763-9808"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Yoochan Myung","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC, Australia"],"raw_orcid":"https://orcid.org/0000-0002-6763-9808","affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071950872","display_name":"Douglas E. V. Pires","orcid":"https://orcid.org/0000-0002-3004-2119"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Douglas E V Pires","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC, Australia","School of Chemistry and Molecular Biosciences, University Of Queensland, St Lucia, QLD, Australia","School of Computing and Information Systems, University of Melbourne , Melbourne, VIC, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC, Australia"],"raw_orcid":"https://orcid.org/0000-0002-3004-2119","affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University Of Queensland, St Lucia, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"School of Computing and Information Systems, University of Melbourne , Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091903225","display_name":"David B. Ascher","orcid":"https://orcid.org/0000-0003-2948-2413"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"David B Ascher","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC, Australia","School of Chemistry and Molecular Biosciences, University Of Queensland, St Lucia, QLD, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC, Australia"],"raw_orcid":"https://orcid.org/0000-0003-2948-2413","affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute , Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University Of Queensland, St Lucia, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071950872","https://openalex.org/A5091903225"],"corresponding_institution_ids":["https://openalex.org/I142471025","https://openalex.org/I165143802","https://openalex.org/I165779595"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":null,"fwci":6.117,"has_fulltext":false,"cited_by_count":78,"citation_normalized_percentile":{"value":0.97225172,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"38","issue":"4","first_page":"1141","last_page":"1143"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.6674000024795532,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.6674000024795532,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.295199990272522,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.006399999838322401,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7528418302536011},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.716194748878479},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.61101233959198},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5340418219566345},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.4365918040275574},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4141223430633545},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3606029152870178},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33876317739486694},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.22822502255439758},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1702759861946106},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1615246832370758},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08893007040023804}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7528418302536011},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.716194748878479},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.61101233959198},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5340418219566345},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.4365918040275574},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4141223430633545},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3606029152870178},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33876317739486694},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.22822502255439758},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1702759861946106},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1615246832370758},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08893007040023804},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","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},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000941","descriptor_name":"Antigens","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000941","descriptor_name":"Antigens","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000941","descriptor_name":"Antigens","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":"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:10.1093/bioinformatics/btab762","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab762","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34734992","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34734992","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2033211519","https://openalex.org/W2130675979","https://openalex.org/W2346940354","https://openalex.org/W2400041270","https://openalex.org/W2508425869","https://openalex.org/W2750875483","https://openalex.org/W2911741628","https://openalex.org/W2915344963","https://openalex.org/W2980372463","https://openalex.org/W2996908194","https://openalex.org/W3026328277"],"related_works":["https://openalex.org/W3187200704","https://openalex.org/W2031259671","https://openalex.org/W3112966125","https://openalex.org/W2108080735","https://openalex.org/W1990832091","https://openalex.org/W2095596733","https://openalex.org/W4240532245","https://openalex.org/W1966443150","https://openalex.org/W2024917329","https://openalex.org/W1990685384"],"abstract_inverted_index":{"MOTIVATION:":[0],"Understanding":[1],"antibody-antigen":[2,74],"interactions":[3],"is":[4,136],"key":[5],"to":[6,41,52,95,124],"improving":[7],"their":[8],"binding":[9,29,45,75],"affinities":[10],"and":[11,49,51,144],"specificities.":[12],"While":[13],"experimental":[14,32],"approaches":[15],"are":[16,152],"fundamental":[17],"for":[18,58],"developing":[19],"new":[20,130],"therapeutics,":[21],"computational":[22],"methods":[23,88],"can":[24,104],"provide":[25],"quick":[26],"assessment":[27],"of":[28,61,72,93,129],"landscapes,":[30],"guiding":[31],"design.":[33],"Despite":[34],"this,":[35],"little":[36],"effort":[37],"has":[38],"been":[39],"devoted":[40],"accurately":[42,105],"predicting":[43,73],"the":[44,127],"affinity":[46,76],"between":[47],"antibodies":[48],"antigens":[50],"develop":[53],"tailored":[54],"docking":[55,113],"scoring":[56,114],"functions":[57],"this":[59],"type":[60],"interaction.":[62],"Here,":[63],"we":[64],"developed":[65],"CSM-AB,":[66],"a":[67,90,112,140],"machine":[68],"learning":[69],"method":[70],"capable":[71],"by":[77],"modelling":[78],"interaction":[79],"interfaces":[80],"as":[81,111,139],"graph-based":[82],"signatures.":[83],"RESULTS:":[84],"CSM-AB":[85,103,118,135],"outperformed":[86],"alternative":[87],"achieving":[89],"Pearson's":[91],"correlation":[92],"up":[94],"0.64":[96],"on":[97],"blind":[98],"tests.":[99],"We":[100,116],"also":[101],"show":[102],"rank":[106],"near-native":[107],"poses,":[108],"working":[109],"effectively":[110],"function.":[115],"believe":[117],"will":[119],"be":[120],"an":[121],"invaluable":[122],"tool":[123],"assist":[125],"in":[126],"development":[128],"immunotherapies.":[131],"AVAILABILITY":[132],"AND":[133],"IMPLEMENTATION:":[134],"freely":[137],"available":[138,153],"user-friendly":[141],"web":[142],"interface":[143],"API":[145],"at":[146,154],"http://biosig.unimelb.edu.au/csm_ab/datasets.":[147],"SUPPLEMENTARY":[148],"INFORMATION:":[149],"Supplementary":[150],"data":[151],"Bioinformatics":[155],"online.":[156]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":28},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":5}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
