{"id":"https://openalex.org/W2122348262","doi":"https://doi.org/10.1186/1756-0381-2-8","title":"3PFDB - A database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach","display_name":"3PFDB - A database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach","publication_year":2009,"publication_date":"2009-12-01","ids":{"openalex":"https://openalex.org/W2122348262","doi":"https://doi.org/10.1186/1756-0381-2-8","mag":"2122348262","pmid":"https://pubmed.ncbi.nlm.nih.gov/19961575"},"language":"en","primary_location":{"id":"doi:10.1186/1756-0381-2-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-2-8","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-2-8","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-2-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016416266","display_name":"Khader Shameer","orcid":"https://orcid.org/0000-0002-9982-1911"},"institutions":[{"id":"https://openalex.org/I11947397","display_name":"Tata Institute of Fundamental Research","ror":"https://ror.org/03ht1xw27","country_code":"IN","type":"education","lineage":["https://openalex.org/I11947397","https://openalex.org/I2799351866","https://openalex.org/I3149292468"]},{"id":"https://openalex.org/I194223965","display_name":"National Centre for Biological Sciences","ror":"https://ror.org/03gf8rp76","country_code":"IN","type":"facility","lineage":["https://openalex.org/I11947397","https://openalex.org/I194223965","https://openalex.org/I2799351866","https://openalex.org/I3149292468"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Khader Shameer","raw_affiliation_strings":["National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary road, Bangalore 560065, India","National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bangalore, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary road, Bangalore 560065, India","institution_ids":["https://openalex.org/I194223965"]},{"raw_affiliation_string":"National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bangalore, India","institution_ids":["https://openalex.org/I194223965","https://openalex.org/I11947397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052465605","display_name":"Nagarajan Paramasivam","orcid":"https://orcid.org/0000-0002-7126-8472"},"institutions":[{"id":"https://openalex.org/I11947397","display_name":"Tata Institute of Fundamental Research","ror":"https://ror.org/03ht1xw27","country_code":"IN","type":"education","lineage":["https://openalex.org/I11947397","https://openalex.org/I2799351866","https://openalex.org/I3149292468"]},{"id":"https://openalex.org/I194223965","display_name":"National Centre for Biological Sciences","ror":"https://ror.org/03gf8rp76","country_code":"IN","type":"facility","lineage":["https://openalex.org/I11947397","https://openalex.org/I194223965","https://openalex.org/I2799351866","https://openalex.org/I3149292468"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Paramasivam Nagarajan","raw_affiliation_strings":["National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary road, Bangalore, 560065, India","National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bangalore, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary road, Bangalore, 560065, India","institution_ids":["https://openalex.org/I194223965","https://openalex.org/I11947397"]},{"raw_affiliation_string":"National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bangalore, India","institution_ids":["https://openalex.org/I194223965","https://openalex.org/I11947397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106940579","display_name":"K. Gaurav","orcid":null},"institutions":[{"id":"https://openalex.org/I11947397","display_name":"Tata Institute of Fundamental Research","ror":"https://ror.org/03ht1xw27","country_code":"IN","type":"education","lineage":["https://openalex.org/I11947397","https://openalex.org/I2799351866","https://openalex.org/I3149292468"]},{"id":"https://openalex.org/I194223965","display_name":"National Centre for Biological Sciences","ror":"https://ror.org/03gf8rp76","country_code":"IN","type":"facility","lineage":["https://openalex.org/I11947397","https://openalex.org/I194223965","https://openalex.org/I2799351866","https://openalex.org/I3149292468"]},{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU","IN"],"is_corresponding":false,"raw_author_name":"Kumar Gaurav","raw_affiliation_strings":["Department of Chemistry and Biomolecular sciences, Macquarie University, Sydney, NSW, Australia","National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary road, Bangalore, 560065, India","Department of Chemistry and Biomolecular sciences, Macquarie University, Sydney, Australia","National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biomolecular sciences, Macquarie University, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I99043593"]},{"raw_affiliation_string":"National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary road, Bangalore, 560065, India","institution_ids":["https://openalex.org/I194223965","https://openalex.org/I11947397"]},{"raw_affiliation_string":"Department of Chemistry and Biomolecular sciences, Macquarie University, Sydney, Australia","institution_ids":["https://openalex.org/I99043593"]},{"raw_affiliation_string":"National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India","institution_ids":["https://openalex.org/I194223965","https://openalex.org/I11947397"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076779054","display_name":"Ramanathan Sowdhamini","orcid":"https://orcid.org/0000-0002-6642-2367"},"institutions":[{"id":"https://openalex.org/I11947397","display_name":"Tata Institute of Fundamental Research","ror":"https://ror.org/03ht1xw27","country_code":"IN","type":"education","lineage":["https://openalex.org/I11947397","https://openalex.org/I2799351866","https://openalex.org/I3149292468"]},{"id":"https://openalex.org/I194223965","display_name":"National Centre for Biological Sciences","ror":"https://ror.org/03gf8rp76","country_code":"IN","type":"facility","lineage":["https://openalex.org/I11947397","https://openalex.org/I194223965","https://openalex.org/I2799351866","https://openalex.org/I3149292468"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Ramanathan Sowdhamini","raw_affiliation_strings":["National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary road, Bangalore, 560065, India","National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bangalore, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary road, Bangalore, 560065, India","institution_ids":["https://openalex.org/I194223965","https://openalex.org/I11947397"]},{"raw_affiliation_string":"National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bangalore, India","institution_ids":["https://openalex.org/I194223965","https://openalex.org/I11947397"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076779054"],"corresponding_institution_ids":["https://openalex.org/I11947397","https://openalex.org/I194223965"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.3798,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.69977836,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"2","issue":"1","first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.2721000015735626,"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"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.2721000015735626,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.23010000586509705,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.13519999384880066,"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/computer-science","display_name":"Computer science","score":0.6581692695617676},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4890967011451721}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6581692695617676},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4890967011451721}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1756-0381-2-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-2-8","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-2-8","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:19961575","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19961575","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":"BioData mining","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.212.8314","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.212.8314","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.biodatamining.org/content/pdf/1756-0381-2-8.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:1b33314de6db41d6b0644b971b53971f","is_oa":false,"landing_page_url":"https://doaj.org/article/1b33314de6db41d6b0644b971b53971f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 2, Iss 1, p 8 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2801675","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2801675","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1756-0381-2-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-2-8","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-2-8","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"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/W2122348262.pdf","grobid_xml":"https://content.openalex.org/works/W2122348262.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W116194421","https://openalex.org/W121670436","https://openalex.org/W1536499467","https://openalex.org/W1585033005","https://openalex.org/W1600814222","https://openalex.org/W1969051510","https://openalex.org/W1969331541","https://openalex.org/W1982481323","https://openalex.org/W1990601524","https://openalex.org/W1991741320","https://openalex.org/W1997379747","https://openalex.org/W1998676514","https://openalex.org/W2006941904","https://openalex.org/W2007745123","https://openalex.org/W2015507989","https://openalex.org/W2017664295","https://openalex.org/W2022961047","https://openalex.org/W2024648909","https://openalex.org/W2043816461","https://openalex.org/W2048947602","https://openalex.org/W2053931156","https://openalex.org/W2068745373","https://openalex.org/W2072152013","https://openalex.org/W2095013577","https://openalex.org/W2096234478","https://openalex.org/W2098223336","https://openalex.org/W2103017472","https://openalex.org/W2117249420","https://openalex.org/W2119493141","https://openalex.org/W2121520117","https://openalex.org/W2124457330","https://openalex.org/W2127170489","https://openalex.org/W2133950463","https://openalex.org/W2136280642","https://openalex.org/W2143705344","https://openalex.org/W2149997286","https://openalex.org/W2151831732","https://openalex.org/W2157259034","https://openalex.org/W2158714788","https://openalex.org/W2161062388","https://openalex.org/W2163105490","https://openalex.org/W2505446473","https://openalex.org/W4211054902"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"families":[2,44,107,251],"could":[3],"be":[4,280,300],"related":[5],"to":[6,21,28,100,132,217,230,260,287],"each":[7],"other":[8],"at":[9,23],"broad":[10],"levels":[11],"that":[12,45],"group":[13],"them":[14],"as":[15,48,172,213],"superfamilies.":[16],"These":[17],"relationships":[18],"are":[19,34,46,52,165],"harder":[20],"detect":[22],"the":[24,40,90,102,123,145,188,214,219,232,285,303],"sequence":[25,95,171],"level":[26],"due":[27],"high":[29],"evolutionary":[30,81],"divergence.":[31],"Sequence":[32],"searches":[33,85],"strongly":[35],"directed":[36],"and":[37,55,80,179,263,290],"influenced":[38],"by":[39],"best":[41,152,220,244,268],"representatives":[42],"of":[43,58,64,77,125,149,169,190,243,248,257,267,275],"viewed":[47],"starting":[49,223],"points.":[50],"PSSMs":[51,105,272],"useful":[53,282],"approximations":[54],"mathematical":[56],"representations":[57],"protein":[59,73,130,142,150,250],"alignments,":[60],"with":[61],"wide":[62],"array":[63],"applications":[65],"in":[66,109,163,175,201],"bioinformatics":[67],"approaches":[68],"like":[69],"remote":[70],"homology":[71],"detection,":[72],"family":[74,131,278],"analysis,":[75],"detection":[76],"new":[78],"members":[79],"modelling.":[82],"Computational":[83],"intensive":[84],"have":[86,186],"been":[87,159],"performed":[88],"using":[89,167,183,208,293,302],"neural":[91],"network":[92],"based":[93],"sensitive":[94],"search":[96],"method":[97,210],"called":[98,156],"FASSM":[99,209],"identify":[101,133,218,261],"Best":[103,136],"Representative":[104,137],"for":[106,122,235,273,284],"reported":[108,200],"Pfam":[110,202,253,277],"database":[111,148,203,266],"version":[112],"22.":[113],"RESULTS:":[114],"We":[115,185],"designed":[116],"a":[117,129,134,147,173,176,236,241,264,281],"novel":[118],"data":[119],"mining":[120],"approach":[121,182,259],"assessment":[124],"individual":[126,170],"sequences":[127,193,229],"from":[128,195,224,252],"single":[135],"PSSM":[138,154,161,246,296],"profile":[139,234],"(BRP)":[140],"per":[141],"family.":[143,238],"Using":[144],"approach,":[146],"family-specific":[151],"representative":[153,221,245,269],"profiles":[155,162,247],"3PFDB":[157,164,239,298],"has":[158],"developed.":[160],"curated":[166,265],"performance":[168],"reference":[174],"rigorous":[177],"scoring":[178],"coverage":[180],"analysis":[181,207,292],"FASSM.":[184],"assessed":[187],"suitability":[189],"10,":[191],"85,588":[192],"derived":[194,271],"seed":[196],"or":[197,227],"full":[198,225],"alignments":[199],"(Version":[204],"22).":[205],"Coverage":[206],"is":[211,240],"used":[212],"filtering":[215],"step":[216],"sequence,":[222],"length":[226],"domain":[228],"generate":[231],"final":[233],"given":[237],"collection":[242],"8,524":[249],"database.":[254],"CONCLUSION:":[255],"Availability":[256],"an":[258],"BRPs":[262],"PSI-BLAST":[270],"91.4%":[274],"current":[276],"will":[279],"resource":[283],"community":[286],"perform":[288],"detailed":[289],"specific":[291],"family-specific,":[294],"best-representative":[295],"profiles.":[297],"can":[299],"accessed":[301],"URL:":[304],"http://caps.ncbs.res.in/3pfdb.":[305]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
