{"id":"https://openalex.org/W4367174467","doi":"https://doi.org/10.1093/nar/gkad303","title":"PASSer: fast and accurate prediction of protein allosteric sites","display_name":"PASSer: fast and accurate prediction of protein allosteric sites","publication_year":2023,"publication_date":"2023-04-27","ids":{"openalex":"https://openalex.org/W4367174467","doi":"https://doi.org/10.1093/nar/gkad303","pmid":"https://pubmed.ncbi.nlm.nih.gov/37102691"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkad303","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad303","pdf_url":"https://academic.oup.com/nar/article-pdf/51/W1/W427/50736495/gkad303.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/51/W1/W427/50736495/gkad303.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022395272","display_name":"Hao Tian","orcid":"https://orcid.org/0000-0002-0186-9811"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hao Tian","raw_affiliation_strings":["Department of Chemistry, Center for Research Computing, Center for Drug Discovery , Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75206, USA"],"raw_orcid":"https://orcid.org/0000-0002-0186-9811","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Center for Research Computing, Center for Drug Discovery , Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75206, USA","institution_ids":["https://openalex.org/I178169726"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013883660","display_name":"Sian Xiao","orcid":"https://orcid.org/0000-0002-3451-5227"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sian Xiao","raw_affiliation_strings":["Department of Chemistry, Center for Research Computing, Center for Drug Discovery , Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75206, USA"],"raw_orcid":"https://orcid.org/0000-0002-3451-5227","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Center for Research Computing, Center for Drug Discovery , Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75206, USA","institution_ids":["https://openalex.org/I178169726"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028757824","display_name":"Xi Jiang","orcid":"https://orcid.org/0000-0002-2754-0862"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xi Jiang","raw_affiliation_strings":["Department of Statistical Science, Southern Methodist University , Dallas, TX 75206, USA"],"raw_orcid":"https://orcid.org/0000-0002-2754-0862","affiliations":[{"raw_affiliation_string":"Department of Statistical Science, Southern Methodist University , Dallas, TX 75206, USA","institution_ids":["https://openalex.org/I178169726"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010373442","display_name":"Peng Tao","orcid":"https://orcid.org/0000-0002-2488-0239"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peng Tao","raw_affiliation_strings":["Department of Chemistry, Center for Research Computing, Center for Drug Discovery , Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75206, USA"],"raw_orcid":"https://orcid.org/0000-0002-2488-0239","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Center for Research Computing, Center for Drug Discovery , Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75206, USA","institution_ids":["https://openalex.org/I178169726"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5022395272"],"corresponding_institution_ids":["https://openalex.org/I178169726"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":12.4012,"has_fulltext":true,"cited_by_count":64,"citation_normalized_percentile":{"value":0.99027483,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"51","issue":"W1","first_page":"W427","last_page":"W431"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9952999949455261,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9607999920845032,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.9481853246688843},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5622957348823547},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4994068145751953},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4841335713863373},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4684121012687683},{"id":"https://openalex.org/keywords/passer","display_name":"Passer","score":0.4443170428276062},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.4220088720321655},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39948534965515137},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39913904666900635},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3372587561607361},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12419202923774719},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09093150496482849}],"concepts":[{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.9481853246688843},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5622957348823547},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4994068145751953},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4841335713863373},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4684121012687683},{"id":"https://openalex.org/C2780148931","wikidata":"https://www.wikidata.org/wiki/Q28753","display_name":"Passer","level":3,"score":0.4443170428276062},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.4220088720321655},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39948534965515137},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39913904666900635},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3372587561607361},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12419202923774719},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09093150496482849},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C2778825724","wikidata":"https://www.wikidata.org/wiki/Q243984","display_name":"Sparrow","level":2,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"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":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkad303","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad303","pdf_url":"https://academic.oup.com/nar/article-pdf/51/W1/W427/50736495/gkad303.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:37102691","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37102691","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10320119","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10320119","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10320119/pdf/gkad303.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkad303","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad303","pdf_url":"https://academic.oup.com/nar/article-pdf/51/W1/W427/50736495/gkad303.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1488049601","display_name":null,"funder_award_id":"R15GM122013","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G706801179","display_name":null,"funder_award_id":"R15GM122013","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4367174467.pdf"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1964286802","https://openalex.org/W2002300224","https://openalex.org/W2003998164","https://openalex.org/W2006782375","https://openalex.org/W2011703027","https://openalex.org/W2029667189","https://openalex.org/W2046468203","https://openalex.org/W2064399386","https://openalex.org/W2074929227","https://openalex.org/W2077912217","https://openalex.org/W2116993067","https://openalex.org/W2125299915","https://openalex.org/W2126586461","https://openalex.org/W2151794181","https://openalex.org/W2157605186","https://openalex.org/W2164088236","https://openalex.org/W2177124199","https://openalex.org/W2254489325","https://openalex.org/W2295598076","https://openalex.org/W2417513559","https://openalex.org/W2620998958","https://openalex.org/W2768348081","https://openalex.org/W2911398658","https://openalex.org/W2945661338","https://openalex.org/W2964015378","https://openalex.org/W3080555959","https://openalex.org/W3088730103","https://openalex.org/W3130442532","https://openalex.org/W4200375412","https://openalex.org/W4285009335","https://openalex.org/W4287826698","https://openalex.org/W4292264864","https://openalex.org/W4307122328","https://openalex.org/W4312045153","https://openalex.org/W4320341731","https://openalex.org/W6726873649","https://openalex.org/W6745609711","https://openalex.org/W6774581290","https://openalex.org/W6781932242"],"related_works":["https://openalex.org/W3126783617","https://openalex.org/W2732388178","https://openalex.org/W3093468851","https://openalex.org/W4353055924","https://openalex.org/W2806488847","https://openalex.org/W2121688928","https://openalex.org/W2772651271","https://openalex.org/W2769925250","https://openalex.org/W4361279638","https://openalex.org/W4313452391"],"abstract_inverted_index":{"Allostery":[0],"refers":[1],"to":[2,12],"the":[3,20,116,154,159],"biological":[4],"process":[5,35],"by":[6],"which":[7],"an":[8,82,96,136],"effector":[9],"modulator":[10],"binds":[11],"a":[13,16,39,59,105,148],"protein":[14,112,141],"at":[15,57],"site":[17,67],"distant":[18],"from":[19,115],"active":[21],"site,":[22],"known":[23],"as":[24,145,147],"allosteric":[25,28,34,43,66],"site.":[26],"Identifying":[27],"sites":[29],"is":[30,37],"essential":[31],"for":[32,62],"discovering":[33],"and":[36,64,69,76,90,103,125,142,176],"considered":[38],"critical":[40],"factor":[41],"in":[42,135,172],"drug":[44],"development.":[45],"To":[46,162],"facilitate":[47],"related":[48],"research,":[49],"we":[50],"developed":[51],"PASSer":[52,110,164],"(Protein":[53],"Allosteric":[54],"Sites":[55],"Server)":[56],"https://passer.smu.edu,":[58],"web":[60],"application":[61],"fast":[63],"accurate":[65],"prediction":[68],"visualization.":[70],"The":[71,131],"website":[72],"hosts":[73],"three":[74,156],"trained":[75],"published":[77],"machine":[78,98],"learning":[79,84,99],"models:":[80],"(i)":[81],"ensemble":[83],"model":[85,100,107],"with":[86,101,108,158],"extreme":[87],"gradient":[88],"boosting":[89],"graph":[91],"convolutional":[92],"neural":[93],"network,":[94],"(ii)":[95],"automated":[97],"AutoGluon":[102],"(iii)":[104],"learning-to-rank":[106],"LambdaMART.":[109],"accepts":[111],"entries":[113],"directly":[114],"Protein":[117],"Data":[118],"Bank":[119],"(PDB)":[120],"or":[121],"user-uploaded":[122],"PDB":[123],"files,":[124],"can":[126],"conduct":[127],"predictions":[128,152],"within":[129],"seconds.":[130],"results":[132],"are":[133],"presented":[134],"interactive":[137],"window":[138],"that":[139,150],"displays":[140],"pockets'":[143],"structures,":[144],"well":[146],"table":[149],"summarizes":[151],"of":[153],"top":[155],"pockets":[157],"highest":[160],"probabilities/scores.":[161],"date,":[163],"has":[165,177],"been":[166],"visited":[167],"over":[168,173,179],"49":[169],"000":[170],"times":[171],"70":[174],"countries":[175],"executed":[178],"6":[180],"200":[181],"jobs.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":27},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":11}],"updated_date":"2026-04-25T08:17:42.794288","created_date":"2025-10-10T00:00:00"}
