{"id":"https://openalex.org/W2089085945","doi":"https://doi.org/10.1093/nar/gkh430","title":"FATCAT: a web server for flexible structure comparison and structure similarity searching","display_name":"FATCAT: a web server for flexible structure comparison and structure similarity searching","publication_year":2004,"publication_date":"2004-07-01","ids":{"openalex":"https://openalex.org/W2089085945","doi":"https://doi.org/10.1093/nar/gkh430","mag":"2089085945","pmid":"https://pubmed.ncbi.nlm.nih.gov/15215455"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkh430","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh430","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_2/W582/6210251/gkh430.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":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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/nar/article-pdf/32/suppl_2/W582/6210251/gkh430.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010000042","display_name":"Y. Ye","orcid":null},"institutions":[{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I40399489","display_name":"Torrey Pines Institute For Molecular Studies","ror":"https://ror.org/01grq2104","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40399489"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Y. Ye","raw_affiliation_strings":["The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA. yye@burnham.org","The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA. yye@burnham.org","institution_ids":["https://openalex.org/I188891513"]},{"raw_affiliation_string":"The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla CA 92037, USA","institution_ids":["https://openalex.org/I188891513","https://openalex.org/I40399489"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010671148","display_name":"Adam Godzik","orcid":"https://orcid.org/0000-0002-2425-852X"},"institutions":[{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I40399489","display_name":"Torrey Pines Institute For Molecular Studies","ror":"https://ror.org/01grq2104","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40399489"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Godzik","raw_affiliation_strings":["The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037 USA","The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037 USA","institution_ids":["https://openalex.org/I188891513"]},{"raw_affiliation_string":"The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla CA 92037, USA","institution_ids":["https://openalex.org/I188891513","https://openalex.org/I40399489"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5010000042"],"corresponding_institution_ids":["https://openalex.org/I188891513","https://openalex.org/I40399489"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":1.9295,"has_fulltext":true,"cited_by_count":338,"citation_normalized_percentile":{"value":0.85085126,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"32","issue":"Web Server","first_page":"W582","last_page":"W585"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983999729156494,"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":0.9983999729156494,"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":0.998199999332428,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9817000031471252,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.7181079387664795},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.7157436609268188},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.7018471956253052},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6773656606674194},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6136890649795532},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.5568526387214661},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5367385745048523},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.49151691794395447},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.46546104550361633},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.4507283866405487},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.41718268394470215},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4026721715927124},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3477620482444763},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.24434539675712585},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2210141122341156},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.13326358795166016},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.105680912733078},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10198205709457397},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09074532985687256},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.0884409248828888},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.07789993286132812}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7181079387664795},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.7157436609268188},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.7018471956253052},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6773656606674194},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6136890649795532},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.5568526387214661},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5367385745048523},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.49151691794395447},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.46546104550361633},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.4507283866405487},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.41718268394470215},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4026721715927124},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3477620482444763},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.24434539675712585},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2210141122341156},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.13326358795166016},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.105680912733078},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10198205709457397},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09074532985687256},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0884409248828888},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.07789993286132812},{"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":[{"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":"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":"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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkh430","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh430","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_2/W582/6210251/gkh430.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":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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15215455","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15215455","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:10.1.1.97.7996","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.97.7996","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/reprint/32/suppl_2/W582.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:441568","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/441568","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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkh430","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh430","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_2/W582/6210251/gkh430.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":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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2089085945.pdf","grobid_xml":"https://content.openalex.org/works/W2089085945.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1582255757","https://openalex.org/W1590165017","https://openalex.org/W1965910641","https://openalex.org/W1966190762","https://openalex.org/W1966521833","https://openalex.org/W2022058405","https://openalex.org/W2022402206","https://openalex.org/W2040770994","https://openalex.org/W2050330741","https://openalex.org/W2085277871","https://openalex.org/W2087151779","https://openalex.org/W2093547815","https://openalex.org/W2097642323","https://openalex.org/W2117239890","https://openalex.org/W2130479394","https://openalex.org/W2152326664"],"related_works":["https://openalex.org/W4388749535","https://openalex.org/W2121688928","https://openalex.org/W4389309199","https://openalex.org/W4285340733","https://openalex.org/W2584773272","https://openalex.org/W4375844720","https://openalex.org/W1897312405","https://openalex.org/W2084743099","https://openalex.org/W4235583582","https://openalex.org/W2803843415"],"abstract_inverted_index":{"Protein":[0,106],"structure":[1,63,89,159,191,199],"comparison,":[2],"an":[3],"important":[4],"problem":[5],"in":[6,18,74,137,150,197],"structural":[7,52,114],"biology,":[8],"has":[9],"two":[10,15,75,83,101],"main":[11],"applications:":[12],"(i)":[13],"comparing":[14],"protein":[16,62,76,102,167],"structures":[17,32,103,135,149,168],"order":[19],"to":[20,34,82,172,194],"identify":[21],"the":[22,58,105,117,122,131,134,142,147,161,173,177,185,189,198],"similarities":[23],"and":[24,28,71,91,116,160],"differences":[25],"between":[26],"them,":[27],"(ii)":[29],"searching":[30,95],"for":[31,41,86,93,96],"similar":[33,98,171],"a":[35,126,164],"query":[36,158,190],"structure.":[37],"Many":[38],"web-based":[39],"resources":[40],"both":[42],"applications":[43],"are":[44,48,170],"available,":[45],"but":[46],"all":[47],"based":[49],"on":[50],"rigid":[51],"alignment":[53,115],"algorithms.":[54],"FATCAT":[55,181,201],"server":[56,79,162,182,202],"implements":[57],"recently":[59],"developed":[60],"flexible":[61,88],"comparison":[64,90],"algorithm":[65],"FATCAT,":[66],"which":[67],"automatically":[68],"identifies":[69],"hinges":[70],"internal":[72],"rearrangements":[73],"structures.":[77],"The":[78],"provides":[80],"access":[81],"algorithms:":[84],"FATCAT-pairwise":[85,111],"pairwise":[87],"FATCAT-search":[92],"database":[94],"structurally":[97],"proteins.":[99],"Given":[100],"[in":[104],"Data":[107],"Bank":[108],"(PDB)":[109],"format],":[110],"reports":[112],"their":[113],"corresponding":[118],"statistical":[119],"significance":[120],"of":[121,133,166,188],"similarity":[123],"measured":[124],"as":[125,192],"P-value.":[127],"Users":[128],"can":[129,183],"view":[130],"superposition":[132],"online":[136],"web":[138],"browsers":[139],"that":[140,169],"support":[141],"Chime":[143],"plug-in,":[144],"or":[145],"download":[146],"superimposed":[148],"PDB":[151],"format.":[152],"In":[153,179],"FATCAT-search,":[154],"users":[155],"provide":[156],"one":[157],"returns":[163],"list":[165],"query,":[174],"ordered":[175],"by":[176],"P-values.":[178],"addition,":[180],"report":[184],"conformational":[186],"changes":[187],"compared":[193],"other":[195],"proteins":[196],"database.":[200],"is":[203],"available":[204],"at":[205],"http://fatcat.burnham.org.":[206]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":22},{"year":2020,"cited_by_count":36},{"year":2019,"cited_by_count":31},{"year":2018,"cited_by_count":18},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":21},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":18},{"year":2012,"cited_by_count":12}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}