{"id":"https://openalex.org/W2160299673","doi":"https://doi.org/10.1093/nar/gkl199","title":"Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet","display_name":"Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet","publication_year":2006,"publication_date":"2006-07-01","ids":{"openalex":"https://openalex.org/W2160299673","doi":"https://doi.org/10.1093/nar/gkl199","mag":"2160299673","pmid":"https://pubmed.ncbi.nlm.nih.gov/16844973"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl199","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl199","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W119/7623064/gkl199.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":true,"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":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W119/7623064/gkl199.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035042265","display_name":"Manoj Tyagi","orcid":"https://orcid.org/0009-0002-8087-0542"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"M. Tyagi","raw_affiliation_strings":["Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102473032","display_name":"Parakh Sharma","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"P. Sharma","raw_affiliation_strings":["Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059401323","display_name":"C. S. Swamy","orcid":"https://orcid.org/0009-0009-2774-1523"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"C. S. Swamy","raw_affiliation_strings":["Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India"],"affiliations":[{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012201029","display_name":"Fr\u00e9d\u00e9ric Cadet","orcid":"https://orcid.org/0000-0002-3568-9595"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"F. Cadet","raw_affiliation_strings":["Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076920718","display_name":"Narayanaswamy Srinivasan","orcid":"https://orcid.org/0000-0002-6566-6239"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"N. Srinivasan","raw_affiliation_strings":["Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India","Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France"],"affiliations":[{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024376929","display_name":"Alexandre G. de Brevern","orcid":"https://orcid.org/0000-0001-7112-5626"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. G. de Brevern","raw_affiliation_strings":["Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101918365","display_name":"Bernard Offmann","orcid":"https://orcid.org/0000-0002-6845-5883"},"institutions":[{"id":"https://openalex.org/I4210113863","display_name":"G\u00e9nomique Bioinformatique et Applications","ror":"https://ror.org/0264vhs54","country_code":"FR","type":"facility","lineage":["https://openalex.org/I124158823","https://openalex.org/I4210113863","https://openalex.org/I4210134562"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"B. Offmann","raw_affiliation_strings":["Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France","INSERM, U726, Equipe de Bioinformatique et G\u00e9nomique Mol\u00e9culaire (EBGM),","Universit\u00e9 Paris 7 -Denis Diderot, case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Biochimie et G\u00e9n\u00e9tique Mol\u00e9culaire, Bioinformatics Team, Universit\u00e9 de La R\u00e9union, BP 7151, 15 avenue Ren\u00e9 Cassin, 97715 Saint Denis Messag Cedex 09, La R\u00e9union, France","institution_ids":[]},{"raw_affiliation_string":"INSERM, U726, Equipe de Bioinformatique et G\u00e9nomique Mol\u00e9culaire (EBGM),","institution_ids":["https://openalex.org/I4210113863","https://openalex.org/I154526488"]},{"raw_affiliation_string":"Universit\u00e9 Paris 7 -Denis Diderot, case 7113, 2, place Jussieu, 75251 Paris Cedex 05, France","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5035042265"],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.8604,"has_fulltext":false,"cited_by_count":56,"citation_normalized_percentile":{"value":0.90700367,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"34","issue":"Web Server","first_page":"W119","last_page":"W123"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9984999895095825,"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":0.9984999895095825,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9983000159263611,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976000189781189,"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/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5894392132759094},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.550190806388855},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5463129281997681},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.528928816318512},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.4822405278682709},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.480591744184494},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.46987658739089966},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46723753213882446},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.45946502685546875},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.444222629070282},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.432483047246933},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4201815724372864},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3883267045021057},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33676183223724365},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2273167371749878},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20759758353233337},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16484218835830688},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12683308124542236},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10698902606964111},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.103054940700531},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09677135944366455},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.07766768336296082}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5894392132759094},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.550190806388855},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5463129281997681},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.528928816318512},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.4822405278682709},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.480591744184494},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.46987658739089966},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46723753213882446},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.45946502685546875},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.444222629070282},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.432483047246933},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4201815724372864},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3883267045021057},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33676183223724365},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2273167371749878},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20759758353233337},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16484218835830688},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12683308124542236},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10698902606964111},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.103054940700531},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09677135944366455},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.07766768336296082}],"mesh":[{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","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":"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},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","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":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}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gkl199","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl199","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W119/7623064/gkl199.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":true,"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:16844973","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16844973","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:eprints.iisc.ac.in:30555","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196309","display_name":"NOT FOUND REPOSITORY (Indian Institute of Science Bangalore)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I59270414","host_organization_name":"Indian Institute of Science Bangalore","host_organization_lineage":["https://openalex.org/I59270414"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.106.596","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.106.596","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/34/suppl_2/W119.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.97.145","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.97.145","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/screenpdf/34/suppl_2/W119.pdf","raw_type":"text"},{"id":"pmh:oai:HAL:inserm-00133751v1","is_oa":true,"landing_page_url":"https://inserm.hal.science/inserm-00133751","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 2006, 34 (Web Server issue), pp.W119-23. ⟨10.1093/nar/gkl199⟩","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:1538797","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkl199","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkl199","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl199","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W119/7623064/gkl199.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":true,"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":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.5099999904632568}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160299673.pdf","grobid_xml":"https://content.openalex.org/works/W2160299673.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1483749025","https://openalex.org/W1520321564","https://openalex.org/W1604980477","https://openalex.org/W1606011614","https://openalex.org/W1899703372","https://openalex.org/W1965910641","https://openalex.org/W1970197953","https://openalex.org/W1976499789","https://openalex.org/W2008393730","https://openalex.org/W2022058405","https://openalex.org/W2041149980","https://openalex.org/W2060589515","https://openalex.org/W2070693796","https://openalex.org/W2074231493","https://openalex.org/W2075451741","https://openalex.org/W2087064593","https://openalex.org/W2100981947","https://openalex.org/W2117077088","https://openalex.org/W2135484509","https://openalex.org/W2141243638","https://openalex.org/W2145358391","https://openalex.org/W2147859827","https://openalex.org/W2150627302","https://openalex.org/W2152655599","https://openalex.org/W2157242929","https://openalex.org/W2160951461","https://openalex.org/W2178327086","https://openalex.org/W4235848672"],"related_works":["https://openalex.org/W1741740882","https://openalex.org/W2070955689","https://openalex.org/W2464527288","https://openalex.org/W2398461637","https://openalex.org/W2136856901","https://openalex.org/W1989090710","https://openalex.org/W4313591132","https://openalex.org/W1493412556","https://openalex.org/W2053260890","https://openalex.org/W2134776608"],"abstract_inverted_index":{"Encoding":[0],"protein":[1,42,86,98,125],"3D":[2],"structures":[3,43,94,99,126,146],"into":[4,116],"1D":[5],"string":[6],"using":[7,54],"short":[8],"structural":[9,12,33,101],"prototypes":[10],"or":[11],"alphabets":[13],"opens":[14],"a":[15,38,59,105,138,159],"new":[16],"front":[17],"for":[18,62,140,144],"structure":[19,87],"comparison":[20,91,122],"and":[21,95,171,179],"analysis.":[22],"Using":[23],"the":[24,69,83,129,149],"well-documented":[25],"16":[26],"motifs":[27],"of":[28,49,85,92,97,118,123,131,151,162,172],"Protein":[29,73],"Blocks":[30],"(PBs)":[31],"as":[32,47,90],"alphabet,":[34],"we":[35],"have":[36],"developed":[37],"methodology":[39,65],"to":[40,111,158],"compare":[41],"that":[44,103],"are":[45],"encoded":[46],"sequences":[48,117,165],"PBs":[50],"by":[51],"aligning":[52],"them":[53],"dynamic":[55],"programming":[56],"which":[57],"uses":[58],"substitution":[60],"matrix":[61],"PBs.":[63,119,152],"This":[64],"is":[66,137,184],"implemented":[67],"in":[68,72,82,100],"applications":[70],"available":[71,186],"Block":[74],"Expert":[75],"(PBE)":[76],"server.":[77],"PBE":[78,154,182],"addresses":[79],"common":[80],"issues":[81],"field":[84],"analysis":[88],"such":[89],"proteins":[93],"identification":[96],"databanks":[102],"resemble":[104],"given":[106],"structure.":[107],"PBE-T":[108],"provides":[109,155],"facility":[110,139],"transform":[112],"any":[113],"PDB":[114],"file":[115],"PBE-ALIGNc":[120],"performs":[121],"two":[124],"based":[127,147],"on":[128,148],"alignment":[130,150],"their":[132],"corresponding":[133],"PB":[134,164,175],"sequences.":[135],"PBE-ALIGNm":[136],"mining":[141],"SCOP":[142,167],"database":[143,160],"similar":[145],"Besides,":[153],"an":[156],"interface":[157],"(PBE-SAdb)":[161],"preprocessed":[163],"from":[166],"culled":[168],"at":[169,177,187],"95%":[170],"all-against-all":[173],"pairwise":[174],"alignments":[176],"family":[178],"superfamily":[180],"levels.":[181],"server":[183],"freely":[185],"http://bioinformatics.univ-reunion.fr/PBE/.":[188]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}