{"id":"https://openalex.org/W4223983421","doi":"https://doi.org/10.1142/s0219720022400029","title":"RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families","display_name":"RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families","publication_year":2022,"publication_date":"2022-04-14","ids":{"openalex":"https://openalex.org/W4223983421","doi":"https://doi.org/10.1142/s0219720022400029","pmid":"https://pubmed.ncbi.nlm.nih.gov/35430947"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720022400029","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720022400029","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033943390","display_name":"Qingting Wei","orcid":"https://orcid.org/0000-0002-8051-8955"},"institutions":[{"id":"https://openalex.org/I141649914","display_name":"Nanchang University","ror":"https://ror.org/042v6xz23","country_code":"CN","type":"education","lineage":["https://openalex.org/I141649914"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingting Wei","raw_affiliation_strings":["School of Software, Nanchang University, Nanchang 330047, Jiangxi Province, P. R. China"],"affiliations":[{"raw_affiliation_string":"School of Software, Nanchang University, Nanchang 330047, Jiangxi Province, P. R. China","institution_ids":["https://openalex.org/I141649914"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113756416","display_name":"Hong Zou","orcid":"https://orcid.org/0000-0002-0930-4444"},"institutions":[{"id":"https://openalex.org/I4210114416","display_name":"Jiangxi Chest Hospital","ror":"https://ror.org/02895kk89","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210114416"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong Zou","raw_affiliation_strings":["Jiangxi Provincial Armed Force Unit Hospital, Nanchang 330043, Jiangxi Province, P. R. China"],"affiliations":[{"raw_affiliation_string":"Jiangxi Provincial Armed Force Unit Hospital, Nanchang 330043, Jiangxi Province, P. R. China","institution_ids":["https://openalex.org/I4210114416"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055955475","display_name":"Cuncong Zhong","orcid":"https://orcid.org/0000-0002-8777-082X"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cuncong Zhong","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, KS 66045, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, KS 66045, USA","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103199933","display_name":"Jianfeng Xu","orcid":"https://orcid.org/0000-0001-9356-9447"},"institutions":[{"id":"https://openalex.org/I141649914","display_name":"Nanchang University","ror":"https://ror.org/042v6xz23","country_code":"CN","type":"education","lineage":["https://openalex.org/I141649914"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianfeng Xu","raw_affiliation_strings":["School of Software, Nanchang University, Nanchang 330047, Jiangxi Province, P. R. China"],"affiliations":[{"raw_affiliation_string":"School of Software, Nanchang University, Nanchang 330047, Jiangxi Province, P. R. China","institution_ids":["https://openalex.org/I141649914"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5103199933"],"corresponding_institution_ids":["https://openalex.org/I141649914"],"apc_list":null,"apc_paid":null,"fwci":0.4289,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.57288721,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"04","first_page":"2240002","last_page":"2240002"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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/T11617","display_name":"Enzyme Production and Characterization","score":0.9873999953269958,"subfield":{"id":"https://openalex.org/subfields/1305","display_name":"Biotechnology"},"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/T12827","display_name":"Biochemical and Molecular Research","score":0.9785000085830688,"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/sequence","display_name":"Sequence (biology)","score":0.6575330495834351},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.6031815409660339},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5705444812774658},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4676275849342346},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4105813503265381},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.30122652649879456},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30005311965942383},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13679185509681702}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6575330495834351},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.6031815409660339},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5705444812774658},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4676275849342346},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4105813503265381},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.30122652649879456},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30005311965942383},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13679185509681702}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720022400029","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720022400029","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:35430947","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35430947","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G287594726","display_name":null,"funder_award_id":"20202BAB202018","funder_id":"https://openalex.org/F4320322665","funder_display_name":"Natural Science Foundation of Jiangxi Province"},{"id":"https://openalex.org/G379471853","display_name":null,"funder_award_id":"61763031","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322665","display_name":"Natural Science Foundation of Jiangxi Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W50958651","https://openalex.org/W1870852322","https://openalex.org/W2021677726","https://openalex.org/W2033339460","https://openalex.org/W2102231637","https://openalex.org/W2105006906","https://openalex.org/W2106882534","https://openalex.org/W2127322768","https://openalex.org/W2132926880","https://openalex.org/W2144362290","https://openalex.org/W2144491622","https://openalex.org/W2154036437","https://openalex.org/W2170831688","https://openalex.org/W2171213294","https://openalex.org/W2622814825","https://openalex.org/W2949078712","https://openalex.org/W3095583226","https://openalex.org/W3101667854"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W2141411672"],"abstract_inverted_index":{"High-quality":[0],"multiple":[1],"sequence":[2],"alignments":[3,61,64,98,113,127,133],"can":[4],"provide":[5],"insights":[6],"into":[7],"the":[8,50,54,59,67,77,88,97,101,110,115,122,125,131,137],"architecture":[9],"and":[10,35,83,105,130],"function":[11],"of":[12,26,30,114,124],"protein":[13,51,117],"families.":[14,118],"The":[15],"existing":[16],"MSA":[17,102],"tools":[18,103],"often":[19],"generate":[20],"results":[21],"inconsistent":[22],"with":[23,107],"biological":[24],"distribution":[25],"conserved":[27],"regions":[28],"because":[29],"positioning":[31],"amino":[32],"acid":[33],"residues":[34],"gaps":[36],"only":[37],"by":[38,80,100,128,134],"symbols.":[39],"We":[40],"propose":[41],"RPfam,":[42],"a":[43],"refiner":[44],"towards":[45],"curated-like":[46],"MSAs":[47],"for":[48],"modeling":[49],"families":[52],"in":[53],"Pfam":[55,116],"database.":[56],"RPfam":[57,94,120],"refines":[58],"automatic":[60],"via":[62],"scoring":[63],"based":[65],"on":[66,136],"PFASUM":[68],"matrix,":[69],"restricting":[70],"realignments":[71],"within":[72],"badly":[73],"aligned":[74],"blocks,":[75],"optimizing":[76],"block":[78],"scores":[79],"dynamic":[81],"programming,":[82],"running":[84],"refinements":[85],"iteratively":[86],"using":[87],"Simulated":[89],"Annealing":[90],"algorithm.":[91],"Experiments":[92],"show":[93],"effectively":[95],"refined":[96],"produced":[99],"ClustalO":[104,126],"Muscle":[106,132],"reference":[108],"to":[109],"curated":[111],"seed":[112],"Especially":[119],"improved":[121],"quality":[123],"4.4%":[129],"2.8%":[135],"gp32":[138],"DNA":[139],"binding":[140],"protein-like":[141],"family.":[142],"Supplementary":[143],"Table":[144],"is":[145],"available":[146],"at":[147],"http://www.worldscinet.com/jbcb/.":[148]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
