{"id":"https://openalex.org/W2040481795","doi":"https://doi.org/10.1093/bioinformatics/btu673","title":"FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures","display_name":"FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures","publication_year":2014,"publication_date":"2014-10-15","ids":{"openalex":"https://openalex.org/W2040481795","doi":"https://doi.org/10.1093/bioinformatics/btu673","mag":"2040481795","pmid":"https://pubmed.ncbi.nlm.nih.gov/25322839"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu673","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu673","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/523/49011146/bioinformatics_31_4_523.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/523/49011146/bioinformatics_31_4_523.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066663062","display_name":"Yi-Fei Huang","orcid":"https://orcid.org/0000-0001-5594-6731"},"institutions":[{"id":"https://openalex.org/I98251732","display_name":"McMaster University","ror":"https://ror.org/02fa3aq29","country_code":"CA","type":"education","lineage":["https://openalex.org/I98251732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yi-Fei Huang","raw_affiliation_strings":["1Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada","Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada","institution_ids":["https://openalex.org/I98251732"]},{"raw_affiliation_string":"Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada;","institution_ids":["https://openalex.org/I98251732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047864197","display_name":"G. Brian Golding","orcid":null},"institutions":[{"id":"https://openalex.org/I98251732","display_name":"McMaster University","ror":"https://ror.org/02fa3aq29","country_code":"CA","type":"education","lineage":["https://openalex.org/I98251732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"G. Brian Golding","raw_affiliation_strings":["1Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada","Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada","institution_ids":["https://openalex.org/I98251732"]},{"raw_affiliation_string":"Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada;","institution_ids":["https://openalex.org/I98251732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5047864197"],"corresponding_institution_ids":["https://openalex.org/I98251732"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5356,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.82047518,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"31","issue":"4","first_page":"523","last_page":"531"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.541700005531311,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.541700005531311,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.21220000088214874,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.0803999975323677,"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/inference","display_name":"Inference","score":0.6906114220619202},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6705707907676697},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6053889989852905},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5397573113441467},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5009162425994873},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.48508942127227783},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33996307849884033},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2968046963214874},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.24282792210578918},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2340030074119568}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6906114220619202},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6705707907676697},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6053889989852905},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5397573113441467},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5009162425994873},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.48508942127227783},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33996307849884033},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2968046963214874},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.24282792210578918},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2340030074119568}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btu673","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu673","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/523/49011146/bioinformatics_31_4_523.pdf","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:25322839","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25322839","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":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu673","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu673","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/523/49011146/bioinformatics_31_4_523.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W16338948","https://openalex.org/W1746819321","https://openalex.org/W1965217295","https://openalex.org/W1967293793","https://openalex.org/W1971801835","https://openalex.org/W1987484131","https://openalex.org/W1994954884","https://openalex.org/W2000571781","https://openalex.org/W2005126631","https://openalex.org/W2012345434","https://openalex.org/W2017519756","https://openalex.org/W2019907599","https://openalex.org/W2027036222","https://openalex.org/W2043543538","https://openalex.org/W2045385459","https://openalex.org/W2056521874","https://openalex.org/W2060908449","https://openalex.org/W2077539484","https://openalex.org/W2092414509","https://openalex.org/W2096525273","https://openalex.org/W2096977241","https://openalex.org/W2097706568","https://openalex.org/W2099994229","https://openalex.org/W2102424972","https://openalex.org/W2103546861","https://openalex.org/W2108795433","https://openalex.org/W2113024639","https://openalex.org/W2116099439","https://openalex.org/W2119498937","https://openalex.org/W2124790653","https://openalex.org/W2130397644","https://openalex.org/W2132926880","https://openalex.org/W2140490890","https://openalex.org/W2142726203","https://openalex.org/W2145126338","https://openalex.org/W2146705459","https://openalex.org/W2150444353","https://openalex.org/W2150934173","https://openalex.org/W2168621448","https://openalex.org/W2170968124","https://openalex.org/W2530014580","https://openalex.org/W3199943451","https://openalex.org/W4211049957","https://openalex.org/W4231170962","https://openalex.org/W4231518691","https://openalex.org/W4247614989","https://openalex.org/W4292820908","https://openalex.org/W6647006078","https://openalex.org/W6654563908","https://openalex.org/W6674647444","https://openalex.org/W6679367572","https://openalex.org/W6800717233"],"related_works":["https://openalex.org/W2372267530","https://openalex.org/W2969189870","https://openalex.org/W2965643117","https://openalex.org/W4303857162","https://openalex.org/W2407375987","https://openalex.org/W2505726097","https://openalex.org/W2010643158","https://openalex.org/W3049691116","https://openalex.org/W2106867672","https://openalex.org/W3081214562"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1],"number":[2],"of":[3,39,95,140,172,224],"statistical":[4],"phylogenetic":[5,26],"methods":[6],"have":[7],"been":[8,76],"developed":[9,110],"to":[10,28,51,78,112,133,166,189],"infer":[11,29,79],"conserved":[12,53,80,141],"functional":[13,54,81,142,205],"sites":[14],"or":[15],"regions":[16],"in":[17,42,56,64,83,144,210],"proteins.":[18],"Many":[19],"methods,":[20],"e.g.":[21],"Rate4Site,":[22,190],"apply":[23],"the":[24,36,61,65,88,93,96,117,192,211,222,236],"standard":[25],"models":[27],"site-specific":[30],"substitution":[31,40],"rates":[32,41],"and":[33,102,151,202],"totally":[34],"ignore":[35],"spatial":[37,97],"correlation":[38],"protein":[43,57,84,145],"tertiary":[44,58,85,146],"structures,":[45,86],"which":[46,91,220],"may":[47],"reduce":[48],"their":[49],"power":[50],"identify":[52],"patches":[55,82,143,206],"structures":[59],"when":[60],"sequences":[62],"used":[63],"analysis":[66],"are":[67,215,246],"highly":[68],"similar.":[69],"The":[70,204,229],"3D":[71,193],"sliding":[72,194],"window":[73,89,195],"method":[74,196],"has":[75],"proposed":[77],"but":[87,191],"size,":[90],"reflects":[92],"strength":[94],"correlation,":[98],"must":[99],"be":[100],"predefined":[101],"is":[103,122,162,170,183,197,232],"not":[104],"inferred":[105],"from":[106],"data.":[107],"We":[108],"recently":[109],"GP4Rate":[111,121],"solve":[113],"these":[114],"problems":[115],"under":[116],"Bayesian":[118,138],"framework.":[119],"Unfortunately,":[120],"computationally":[123],"slow.":[124],"Here,":[125],"we":[126],"present":[127],"an":[128],"intuitive":[129],"web":[130,237],"server,":[131],"FuncPatch,":[132],"perform":[134],"a":[135,163,185],"fast":[136],"approximate":[137],"inference":[139],"structures.":[147],"RESULTS:":[148],"Both":[149],"simulations":[150,179],"four":[152,212],"case":[153,213],"studies":[154,214],"based":[155],"on":[156],"empirical":[157],"data":[158,245],"suggest":[159,180],"that":[160,181],"FuncPatch":[161,169,182,201,209,231],"good":[164],"approximation":[165],"GP4Rate.":[167,176],"However,":[168],"orders":[171],"magnitudes":[173],"faster":[174],"than":[175,200],"In":[177],"addition,":[178],"potentially":[184],"useful":[186],"tool":[187],"complementary":[188],"less":[198],"powerful":[199],"Rate4Site.":[203],"predicted":[207],"by":[208,217],"supported":[216],"experimental":[218],"evidence,":[219],"corroborates":[221],"usefulness":[223],"FuncPatch.":[225],"AVAILABILITY":[226],"AND":[227],"IMPLEMENTATION:":[228],"software":[230],"freely":[233],"available":[234,247],"at":[235,248],"site,":[238],"http://info.mcmaster.ca/yifei/FuncPatch":[239],"CONTACT:":[240],"golding@mcmaster.ca":[241],"SUPPLEMENTARY":[242],"INFORMATION:":[243],"Supplementary":[244],"Bioinformatics":[249],"online.":[250]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
