{"id":"https://openalex.org/W2053807201","doi":"https://doi.org/10.1109/bibm.2013.6732456","title":"PBSalign: Sequence-independent local alignment of protein binding sites","display_name":"PBSalign: Sequence-independent local alignment of protein binding sites","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W2053807201","doi":"https://doi.org/10.1109/bibm.2013.6732456","mag":"2053807201"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2013.6732456","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732456","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5101969689","display_name":"Bin Pang","orcid":"https://orcid.org/0000-0003-0298-2047"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bin Pang","raw_affiliation_strings":["Informatics Institute, University of Missouri, Columbia, MO, USA","Inf. Inst., Univ. of Missouri, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Inf. Inst., Univ. of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037702462","display_name":"David Schlessman","orcid":null},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Schlessman","raw_affiliation_strings":["Informatics Institute, University of Missouri, Columbia, MO, USA","[Dept. of Comput. Sci., Univ. of Missouri, Columbia, MO, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"[Dept. of Comput. Sci., Univ. of Missouri, Columbia, MO, USA]","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041954281","display_name":"Xingyan Kuang","orcid":null},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xingyan Kuang","raw_affiliation_strings":["Informatics Institute, University of Missouri, Columbia, MO, USA","Inf. Inst., Univ. of Missouri, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Inf. Inst., Univ. of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028509888","display_name":"Nan Zhao","orcid":"https://orcid.org/0000-0002-7897-2374"},"institutions":[{"id":"https://openalex.org/I99041443","display_name":"Mississippi State University","ror":"https://ror.org/0432jq872","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I99041443"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nan Zhao","raw_affiliation_strings":["Mississippi State University, MS, USA","Mississippi State University; Starkville MS USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mississippi State University, MS, USA","institution_ids":["https://openalex.org/I99041443"]},{"raw_affiliation_string":"Mississippi State University; Starkville MS USA","institution_ids":["https://openalex.org/I99041443"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111762982","display_name":"Daniel Shyu","orcid":null},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Shyu","raw_affiliation_strings":["Purdue University, West Lafayette, IN, USA","Purdue University West Lafayette IN USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]},{"raw_affiliation_string":"Purdue University West Lafayette IN USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022192689","display_name":"Dmitry Korkin","orcid":"https://orcid.org/0000-0002-3875-9085"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmitry Korkin","raw_affiliation_strings":["Department of Computer Science, University of Missouri, Columbia, MO, USA","[Dept. of Comput. Sci., Univ. of Missouri, Columbia, MO, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"[Dept. of Comput. Sci., Univ. of Missouri, Columbia, MO, USA]","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013031415","display_name":"Chi\u2010Ren Shyu","orcid":"https://orcid.org/0000-0001-9197-9522"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chi-Ren Shyu","raw_affiliation_strings":["Department of Computer Science, University of Missouri, Columbia, MO, USA","[Dept. of Comput. Sci., Univ. of Missouri, Columbia, MO, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"[Dept. of Comput. Sci., Univ. of Missouri, Columbia, MO, USA]","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.0253,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.79471753,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"174","issue":null,"first_page":"35","last_page":"42"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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":0.996399998664856,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9897000193595886,"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/structural-alignment","display_name":"Structural alignment","score":0.7647662162780762},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6071717143058777},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5942144393920898},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5238133072853088},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5104338526725769},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5076843500137329},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.4987921714782715},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4656091034412384},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.42118024826049805},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4172874987125397},{"id":"https://openalex.org/keywords/computational-complexity-theory","display_name":"Computational complexity theory","score":0.4129927158355713},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39020782709121704},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35693487524986267},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3345981538295746},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3321910798549652},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.326019287109375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21535897254943848},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.17471221089363098},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.10648337006568909},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09212863445281982}],"concepts":[{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.7647662162780762},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6071717143058777},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5942144393920898},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5238133072853088},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5104338526725769},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5076843500137329},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.4987921714782715},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4656091034412384},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.42118024826049805},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4172874987125397},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.4129927158355713},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39020782709121704},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35693487524986267},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3345981538295746},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3321910798549652},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.326019287109375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21535897254943848},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.17471221089363098},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.10648337006568909},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09212863445281982},{"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},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2013.6732456","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732456","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Responsible consumption and production","score":0.5299999713897705,"id":"https://metadata.un.org/sdg/12"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1585234850","https://openalex.org/W1967538863","https://openalex.org/W1984406447","https://openalex.org/W1987583739","https://openalex.org/W1995954548","https://openalex.org/W2003610577","https://openalex.org/W2006398943","https://openalex.org/W2010485601","https://openalex.org/W2027134752","https://openalex.org/W2030885701","https://openalex.org/W2048089273","https://openalex.org/W2049981393","https://openalex.org/W2074382324","https://openalex.org/W2081771568","https://openalex.org/W2083624955","https://openalex.org/W2085277871","https://openalex.org/W2096694476","https://openalex.org/W2102245393","https://openalex.org/W2105525514","https://openalex.org/W2106929158","https://openalex.org/W2108138353","https://openalex.org/W2108361377","https://openalex.org/W2114917397","https://openalex.org/W2116007667","https://openalex.org/W2122365200","https://openalex.org/W2122718915","https://openalex.org/W2131989561","https://openalex.org/W2137146016","https://openalex.org/W2138770756","https://openalex.org/W2139373949","https://openalex.org/W2144998676","https://openalex.org/W2146899059","https://openalex.org/W2152281406","https://openalex.org/W2159560083","https://openalex.org/W2160429376","https://openalex.org/W2160902835","https://openalex.org/W2162411291","https://openalex.org/W2165558283","https://openalex.org/W2183091601","https://openalex.org/W4293003482","https://openalex.org/W6647113690","https://openalex.org/W6685863130"],"related_works":["https://openalex.org/W2029514038","https://openalex.org/W2051969447","https://openalex.org/W2061567716","https://openalex.org/W2015399150","https://openalex.org/W2009133913","https://openalex.org/W2275032899","https://openalex.org/W2498689255","https://openalex.org/W1741740882","https://openalex.org/W2075451741","https://openalex.org/W2505756865"],"abstract_inverted_index":{"Accurate":[0],"alignment":[1,37,50,119,145,162],"of":[2,18,25,51,80,92,117],"protein-protein":[3,111],"binding":[4,98],"sites":[5,99],"can":[6],"aid":[7],"in":[8,69],"protein":[9,19],"docking":[10],"studies":[11],"and":[12,27,78,82,96,101,127,143,157,170],"constructing":[13],"templates":[14],"for":[15],"predicting":[16],"structure":[17],"complexes,":[20],"along":[21],"with":[22,45,104],"in-depth":[23],"understanding":[24],"evolutionary":[26],"functional":[28],"relationships.":[29],"However,":[30],"over":[31],"the":[32,49,59,135,151,165],"past":[33],"three":[34],"decades,":[35],"structural":[36,144],"algorithms":[38],"have":[39],"focused":[40],"predominantly":[41],"on":[42,48],"global":[43],"alignments":[44,103],"little":[46],"effort":[47],"local":[52],"interfaces.":[53],"In":[54],"this":[55],"paper,":[56],"we":[57],"introduce":[58],"PBSalign":[60,89,123,149],"(Protein-protein":[61],"Binding":[62],"Site":[63],"alignment)":[64],"method,":[65],"which":[66],"integrates":[67],"techniques":[68],"graph":[70],"theory,":[71],"3D":[72],"localized":[73],"shape":[74],"analysis,":[75],"geometric":[76,106],"scoring,":[77],"utilization":[79],"physiochemical":[81],"geometrical":[83],"properties.":[84],"Computational":[85],"results":[86],"demonstrate":[87],"that":[88],"is":[90,124],"capable":[91],"identifying":[93],"similar":[94],"homologous":[95],"analogous":[97],"accurately":[100],"performing":[102],"better":[105,118],"match":[107,137],"measures":[108],"than":[109,130],"existing":[110],"interface":[112],"comparison":[113],"tools.":[114],"The":[115],"proportion":[116],"quality":[120],"generated":[121],"by":[122,134],"46%,":[125],"56%,":[126],"70%":[128],"more":[129],"Align":[131],"as":[132],"judged":[133],"average":[136],"index":[138,141],"(MI),":[139],"similarity":[140],"(SI),":[142],"score":[146],"(SAS),":[147],"respectively.":[148],"provides":[150],"life":[152],"science":[153],"community":[154],"a":[155],"fast":[156],"accurate":[158],"solution":[159],"to":[160],"binding-site":[161],"while":[163],"striking":[164],"balance":[166],"between":[167],"topological":[168],"details":[169],"computational":[171],"complexity.":[172]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
