{"id":"https://openalex.org/W2162987538","doi":"https://doi.org/10.1093/database/bau026","title":"3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families","display_name":"3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2162987538","doi":"https://doi.org/10.1093/database/bau026","mag":"2162987538","pmid":"https://pubmed.ncbi.nlm.nih.gov/24700812"},"language":"en","primary_location":{"id":"doi:10.1093/database/bau026","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau026","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau026/17472314/bau026.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","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/database/article-pdf/doi/10.1093/database/bau026/17472314/bau026.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086160124","display_name":"Agnel Praveen Joseph","orcid":"https://orcid.org/0000-0002-0997-8422"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Agnel P. Joseph","raw_affiliation_strings":["National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India"],"affiliations":[{"raw_affiliation_string":"National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054548116","display_name":"Prashant Shingate","orcid":"https://orcid.org/0000-0003-4883-1279"},"institutions":[{"id":"https://openalex.org/I164861460","display_name":"Manipal Academy of Higher Education","ror":"https://ror.org/02xzytt36","country_code":"IN","type":"education","lineage":["https://openalex.org/I164861460"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Prashant Shingate","raw_affiliation_strings":["Manipal University, Madhav Nagar, Manipal 576104, Karnataka, India","National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India"],"affiliations":[{"raw_affiliation_string":"Manipal University, Madhav Nagar, Manipal 576104, Karnataka, India","institution_ids":["https://openalex.org/I164861460"]},{"raw_affiliation_string":"National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003333635","display_name":"Atul Kumar Upadhyay","orcid":"https://orcid.org/0000-0002-9146-8914"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Atul K. Upadhyay","raw_affiliation_strings":["National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India"],"affiliations":[{"raw_affiliation_string":"National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076779054","display_name":"Ramanathan Sowdhamini","orcid":"https://orcid.org/0000-0002-6642-2367"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. Sowdhamini","raw_affiliation_strings":["National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India"],"affiliations":[{"raw_affiliation_string":"National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5086160124"],"corresponding_institution_ids":[],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.5693,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.68169751,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"2014","issue":null,"first_page":"bau026","last_page":"bau026"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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":0.9986000061035156,"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/T11482","display_name":"RNA modifications and cancer","score":0.9951000213623047,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.993399977684021,"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/identification","display_name":"Identification (biology)","score":0.6964789032936096},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.6580986976623535},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6335760951042175},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6248912215232849},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5999086499214172},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5404260158538818},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4845070242881775},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3537292182445526},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3319408595561981},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23453041911125183},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23042625188827515},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07184451818466187},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07071468234062195}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6964789032936096},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.6580986976623535},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6335760951042175},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6248912215232849},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5999086499214172},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5404260158538818},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4845070242881775},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3537292182445526},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3319408595561981},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23453041911125183},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23042625188827515},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07184451818466187},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07071468234062195},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bau026","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau026","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau026/17472314/bau026.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:24700812","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24700812","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:2957798","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3974335","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bau026","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau026","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau026/17472314/bau026.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320715","display_name":"Tata Institute of Fundamental Research","ror":"https://ror.org/03ht1xw27"},{"id":"https://openalex.org/F4320335065","display_name":"National Centre for Biological Sciences","ror":"https://ror.org/03gf8rp76"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2162987538.pdf","grobid_xml":"https://content.openalex.org/works/W2162987538.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W116194421","https://openalex.org/W1513332069","https://openalex.org/W2038186997","https://openalex.org/W2055043387","https://openalex.org/W2074706385","https://openalex.org/W2085277871","https://openalex.org/W2103017472","https://openalex.org/W2114520383","https://openalex.org/W2117919289","https://openalex.org/W2118907013","https://openalex.org/W2121560377","https://openalex.org/W2122348262","https://openalex.org/W2138122982","https://openalex.org/W2141885858","https://openalex.org/W2152517415","https://openalex.org/W2152770371","https://openalex.org/W2158714788","https://openalex.org/W2605068739","https://openalex.org/W4210623056","https://openalex.org/W4247554111","https://openalex.org/W4251349192","https://openalex.org/W4320301318","https://openalex.org/W6677847280"],"related_works":["https://openalex.org/W2898732673","https://openalex.org/W2410053581","https://openalex.org/W2383658677","https://openalex.org/W3123203398","https://openalex.org/W623104033","https://openalex.org/W1972473893","https://openalex.org/W2466435674","https://openalex.org/W2765200542","https://openalex.org/W2367893528","https://openalex.org/W3107784576"],"abstract_inverted_index":{"Protein":[0],"domain":[1,54,99,278],"families":[2,55,204],"are":[3,208,246],"usually":[4],"classified":[5],"on":[6,60,101,148],"the":[7,61,66,68,74,102,113,120,194,221],"basis":[8,103],"of":[9,11,16,52,63,76,91,104,123,216,256],"similarity":[10,143],"amino":[12],"acid":[13],"sequences.":[14,279],"Selection":[15],"a":[17,42,45,80,89,140,189],"single":[18],"representative":[19,93,164,183,223],"sequence":[20,35,71,77,124,142,184],"for":[21,26,119,134,168,276],"each":[22,97],"family":[23,70,100,136,174,180,198,222,231,253],"provides":[24,163],"targets":[25],"structure":[27,266,272],"determination":[28],"or":[29,73,229,249,273],"modeling":[30],"and":[31,126,132,151,155,166,237],"also":[32,186,260],"enables":[33],"fast":[34],"searches":[36],"to":[37,41,202,262],"associate":[38],"new":[39],"members":[40,64],"family.":[43,81],"Such":[44],"selection":[46],"could":[47],"be":[48],"challenging":[49],"since":[50],"some":[51],"these":[53,257,277],"exhibit":[56],"huge":[57],"variation":[58],"depending":[59],"number":[62],"in":[65,160,188,233],"family,":[67],"average":[69],"length":[72],"extent":[75],"divergence":[78,196],"within":[79],"We":[82],"had":[83],"earlier":[84],"created":[85],"3PFDB":[86],"database":[87,114],"as":[88],"repository":[90],"best":[92],"sequences,":[94],"selected":[95],"from":[96,251],"PFAM":[98,169],"high":[105],"coverage.":[106,181,213],"In":[107],"this":[108,161],"study,":[109,162],"we":[110],"have":[111,263],"improved":[112,154],"using":[115],"more":[116,177],"efficient":[117],"strategies":[118],"initial":[121],"generation":[122],"profiles":[125,167],"implement":[127],"two":[128],"independent":[129],"methods,":[130],"FASSM":[131,146],"HMMER,":[133],"identifying":[135],"members.":[137,199,254],"HMMER":[138],"employs":[139],"global":[141],"search,":[144],"while":[145],"relies":[147],"motif":[149],"identification":[150],"matching.":[152],"This":[153],"updated":[156],"database,":[157],"3PFDB+":[158],"generated":[159],"sequences":[165,207,217,244],"families,":[170],"with":[171,205,211,243],"13":[172],"519":[173],"representatives":[175],"having":[176],"than":[178],"90%":[179],"The":[182,214],"is":[185],"highlighted":[187],"two-dimensional":[190],"plot,":[191],"which":[192,268],"reflects":[193],"relative":[195],"between":[197],"Representatives":[200],"belonging":[201],"small":[203],"short":[206],"mainly":[209],"associated":[210],"low":[212],"set":[215],"not":[218],"recognized":[219],"by":[220],"profiles,":[224],"highlight":[225],"several":[226],"potential":[227],"false":[228],"weak":[230],"associations":[232],"PFAM.":[234],"Partial":[235],"domains":[236],"fragments":[238],"dominate":[239],"such":[240],"cases,":[241],"along":[242],"that":[245],"highly":[247],"diverged":[248],"different":[250,264,270],"other":[252],"Some":[255],"outliers":[258],"were":[259],"predicted":[261],"secondary":[265],"contents,":[267],"reflect":[269],"putative":[271],"functional":[274],"roles":[275],"Database":[280],"URL:":[281],"http://caps.ncbs.res.in/3pfdbplus/.":[282]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}