{"id":"https://openalex.org/W2152444476","doi":"https://doi.org/10.1093/nar/gki585","title":"PRISM: protein interactions by structural matching","display_name":"PRISM: protein interactions by structural matching","publication_year":2005,"publication_date":"2005-07-01","ids":{"openalex":"https://openalex.org/W2152444476","doi":"https://doi.org/10.1093/nar/gki585","mag":"2152444476","pmid":"https://pubmed.ncbi.nlm.nih.gov/15991339"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki585","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki585","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W331/7623809/gki585.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":null,"license_id":null,"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/33/suppl_2/W331/7623809/gki585.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066047156","display_name":"Utkan Ogmen","orcid":null},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"U. Ogmen","raw_affiliation_strings":["Koc University, Center for Computational Biology and Bioinformatics and College of Engineering Rumelifeneri Yolu, Sariyer, Istanbul 34450, Turkey"],"affiliations":[{"raw_affiliation_string":"Koc University, Center for Computational Biology and Bioinformatics and College of Engineering Rumelifeneri Yolu, Sariyer, Istanbul 34450, Turkey","institution_ids":["https://openalex.org/I1351752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057115991","display_name":"\u00d6zlem Keskin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"O. Keskin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069294660","display_name":"Ali Selim Aytuna","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. S. Aytuna","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025357844","display_name":"Ruth Nussinov","orcid":"https://orcid.org/0000-0002-8115-6415"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. Nussinov","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5036278069","display_name":"Attila G\u00fcrsoy","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Gursoy","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5066047156"],"corresponding_institution_ids":["https://openalex.org/I1351752"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.6707,"has_fulltext":false,"cited_by_count":213,"citation_normalized_percentile":{"value":0.93680222,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"Web Server","first_page":"W331","last_page":"W336"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"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":0.9954000115394592,"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/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.7540491819381714},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.7157725691795349},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.6835657358169556},{"id":"https://openalex.org/keywords/prism","display_name":"Prism","score":0.6367586255073547},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.604716956615448},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5712521076202393},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5241280198097229},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4871666133403778},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4780871570110321},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4365542531013489},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.4258446991443634},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.4137137830257416},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1760263741016388},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11185872554779053},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09475350379943848},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08243057131767273}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.7540491819381714},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.7157725691795349},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.6835657358169556},{"id":"https://openalex.org/C67666897","wikidata":"https://www.wikidata.org/wiki/Q165896","display_name":"Prism","level":2,"score":0.6367586255073547},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.604716956615448},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5712521076202393},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5241280198097229},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4871666133403778},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4780871570110321},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4365542531013489},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.4258446991443634},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.4137137830257416},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1760263741016388},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11185872554779053},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09475350379943848},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08243057131767273},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D011487","descriptor_name":"Protein Conformation","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gki585","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki585","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W331/7623809/gki585.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15991339","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15991339","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:CiteSeerX.psu:10.1.1.107.8385","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.107.8385","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/cgi/screenpdf/33/suppl_2/W331.pdf","raw_type":"text"},{"id":"pmh:oai:cdm21054.contentdm.oclc.org:IR/619","is_oa":false,"landing_page_url":"http://doi.org/10.1093/nar/gki585","pdf_url":null,"source":{"id":"https://openalex.org/S4306401341","display_name":"Digital Collections portal (Ko\u00e7 University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1351752","host_organization_name":"Ko\u00e7 University","host_organization_lineage":["https://openalex.org/I1351752"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research","raw_type":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1160261","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1160261","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gki585","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki585","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W331/7623809/gki585.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152444476.pdf","grobid_xml":"https://content.openalex.org/works/W2152444476.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1534782460","https://openalex.org/W1884509322","https://openalex.org/W1965907701","https://openalex.org/W1983102499","https://openalex.org/W1985153601","https://openalex.org/W2007451197","https://openalex.org/W2025120281","https://openalex.org/W2043699100","https://openalex.org/W2051710717","https://openalex.org/W2065304353","https://openalex.org/W2075770210","https://openalex.org/W2094148990","https://openalex.org/W2115156437","https://openalex.org/W2115410056","https://openalex.org/W2130479394","https://openalex.org/W2158714788","https://openalex.org/W2164391585","https://openalex.org/W2166558964","https://openalex.org/W4233751197"],"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":{"Prism":[0],"(http://gordion.hpc.eng.ku.edu.tr/prism)":[1],"is":[2,16,124,128],"a":[3,19,68,118],"website":[4],"for":[5,117,134],"protein":[6,22,44,71],"interface":[7,23,45],"analysis":[8],"and":[9,41],"prediction":[10,57,98],"of":[11,18,49,70,80,92,104,114],"putative":[12,50],"protein-protein":[13,51],"interactions.":[14],"It":[15],"composed":[17],"database":[20],"holding":[21],"structures":[24,72,106],"derived":[25],"from":[26,74],"the":[27,75,78,89,97,102,112,132],"Protein":[28],"Data":[29],"Bank":[30],"(PDB).":[31],"The":[32],"server":[33],"also":[34,60],"includes":[35],"summary":[36],"information":[37],"about":[38],"related":[39],"proteins":[40],"an":[42],"interactive":[43,125],"viewer.":[46],"A":[47],"list":[48,103],"interactions":[52],"obtained":[53,73],"by":[54,130],"running":[55,131],"our":[56],"algorithm":[58,81,99,133],"can":[59,86],"be":[61],"accessed.":[62],"These":[63],"results":[64,113],"are":[65],"applied":[66],"to":[67,107],"set":[69],"PDB":[76],"at":[77],"time":[79],"execution":[82],"(January":[83],"2004).":[84],"Users":[85],"browse":[87],"through":[88],"non-redundant":[90],"dataset":[91],"representative":[93],"interfaces":[94,109],"on":[95],"which":[96],"depends,":[100],"retrieve":[101],"similar":[105],"these":[108],"or":[110],"see":[111],"interaction":[115],"predictions":[116],"particular":[119],"protein.":[120],"Another":[121],"service":[122],"provided":[123],"prediction.":[126],"This":[127],"done":[129],"user":[135],"input":[136],"structures.":[137]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":15},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":13},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":14},{"year":2012,"cited_by_count":15}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
