{"id":"https://openalex.org/W2130940308","doi":"https://doi.org/10.1093/nar/gkr333","title":"iPBA: a tool for protein structure comparison using sequence alignment strategies","display_name":"iPBA: a tool for protein structure comparison using sequence alignment strategies","publication_year":2011,"publication_date":"2011-05-17","ids":{"openalex":"https://openalex.org/W2130940308","doi":"https://doi.org/10.1093/nar/gkr333","mag":"2130940308","pmid":"https://pubmed.ncbi.nlm.nih.gov/21586582"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkr333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr333","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W18/18783400/gkr333.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/39/suppl_2/W18/18783400/gkr333.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060243916","display_name":"Jean\u2010Christophe Gelly","orcid":"https://orcid.org/0000-0001-5138-361X"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210091780","display_name":"Institut National de la Transfusion Sanguine","ror":"https://ror.org/00fh58138","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210091780"]},{"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":["FR","IN"],"is_corresponding":false,"raw_author_name":"Jean-Christophe Gelly","raw_affiliation_strings":["INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromol\u00e9cules Biologiques, Universit\u00e9 Paris Diderot-Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France","Indian Institute of Science Bangalore, Bengaluru, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromol\u00e9cules Biologiques, Universit\u00e9 Paris Diderot-Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210091780"]},{"raw_affiliation_string":"Indian Institute of Science Bangalore, Bengaluru, India","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086160124","display_name":"Agnel Praveen Joseph","orcid":"https://orcid.org/0000-0002-0997-8422"},"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":"Agnel Praveen Joseph","raw_affiliation_strings":["Indian Institute of Science Bangalore, Bengaluru, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indian Institute of Science Bangalore, Bengaluru, India","institution_ids":["https://openalex.org/I59270414"]}]},{"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":"Narayanaswamy Srinivasan","raw_affiliation_strings":["Indian Institute of Science Bangalore, Bengaluru, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indian Institute of Science Bangalore, Bengaluru, India","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024376929","display_name":"Alexandre G. de Brevern","orcid":"https://orcid.org/0000-0001-7112-5626"},"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":"Alexandre G. de Brevern","raw_affiliation_strings":["Indian Institute of Science Bangalore, Bengaluru, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indian Institute of Science Bangalore, Bengaluru, India","institution_ids":["https://openalex.org/I59270414"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.9733,"has_fulltext":false,"cited_by_count":104,"citation_normalized_percentile":{"value":0.96200736,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"39","issue":"suppl_2","first_page":"W18","last_page":"W23"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9969000220298767,"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/biology","display_name":"Biology","score":0.9417341947555542},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6471314430236816},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5794945359230042},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5693034529685974},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5026698112487793},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.47829705476760864},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.43794625997543335},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.4279616177082062},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.4246785342693329},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4229966402053833},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41346466541290283},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.34647154808044434},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.17479759454727173},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15877491235733032},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14458942413330078}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9417341947555542},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6471314430236816},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5794945359230042},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5693034529685974},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5026698112487793},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.47829705476760864},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.43794625997543335},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4279616177082062},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.4246785342693329},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4229966402053833},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41346466541290283},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.34647154808044434},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.17479759454727173},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15877491235733032},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14458942413330078}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, 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":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":8,"locations":[{"id":"doi:10.1093/nar/gkr333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr333","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W18/18783400/gkr333.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:21586582","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21586582","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:39188","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:10.1.1.888.5304","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.888.5304","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/content/39/suppl_2/W18.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.889.1268","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.889.1268","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/content/early/2011/05/17/nar.gkr333.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.894.4996","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.894.4996","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/content/39/suppl_2/W18.full.pdf","raw_type":"text"},{"id":"pmh:oai:HAL:inserm-00646241v1","is_oa":true,"landing_page_url":"https://inserm.hal.science/inserm-00646241","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, 2011, 39 (Web Server issue), pp.W18-23. &#x27E8;10.1093/nar/gkr333&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:3125758","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3125758","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":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/gkr333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr333","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W18/18783400/gkr333.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":[{"id":"https://metadata.un.org/sdg/4","score":0.4099999964237213,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2130940308.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1600613454","https://openalex.org/W1899703372","https://openalex.org/W1965910641","https://openalex.org/W1976499789","https://openalex.org/W1996945721","https://openalex.org/W2000912174","https://openalex.org/W2002419486","https://openalex.org/W2004178884","https://openalex.org/W2008841836","https://openalex.org/W2022058405","https://openalex.org/W2031326247","https://openalex.org/W2031901496","https://openalex.org/W2055302954","https://openalex.org/W2056366317","https://openalex.org/W2061827467","https://openalex.org/W2074231493","https://openalex.org/W2075451741","https://openalex.org/W2085277871","https://openalex.org/W2087064593","https://openalex.org/W2087151779","https://openalex.org/W2092162343","https://openalex.org/W2097311600","https://openalex.org/W2097617783","https://openalex.org/W2097642323","https://openalex.org/W2098125835","https://openalex.org/W2100126267","https://openalex.org/W2100981947","https://openalex.org/W2102245393","https://openalex.org/W2105321472","https://openalex.org/W2108361377","https://openalex.org/W2110397834","https://openalex.org/W2110483430","https://openalex.org/W2114317416","https://openalex.org/W2122464816","https://openalex.org/W2125898812","https://openalex.org/W2142749069","https://openalex.org/W2143695538","https://openalex.org/W2144998676","https://openalex.org/W2152326664","https://openalex.org/W2160299673","https://openalex.org/W2161534992","https://openalex.org/W2161899160"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2029514038","https://openalex.org/W2141411672","https://openalex.org/W2133116680","https://openalex.org/W1482324242","https://openalex.org/W2468116983","https://openalex.org/W2088487249","https://openalex.org/W187239587","https://openalex.org/W2158700816"],"abstract_inverted_index":{"With":[0,66,106],"the":[1,5,109,130,188],"immense":[2],"growth":[3],"in":[4,127],"number":[6],"of":[7,64,111,113,129],"available":[8],"protein":[9,51],"structures,":[10],"fast":[11,172],"and":[12,71,101,125,141,150,157,173],"accurate":[13],"structure":[14,25,56,176],"comparison":[15,177],"has":[16],"been":[17],"essential.":[18],"We":[19],"propose":[20],"an":[21,90],"efficient":[22,174],"method":[23],"for":[24,137,163],"comparison,":[26],"based":[27],"on":[28],"a":[29,36,49,54,61,67,72,171],"structural":[30,39,78],"alphabet.":[31],"Protein":[32],"Blocks":[33],"(PBs)":[34],"is":[35,134,167],"widely":[37],"used":[38],"alphabet":[40],"with":[41],"16":[42],"pentapeptide":[43],"conformations":[44],"that":[45,181],"can":[46,57,192],"fairly":[47],"approximate":[48],"complete":[50],"chain.":[52],"Thus":[53],"3D":[55,152],"be":[58,184,193],"translated":[59],"into":[60],"1D":[62],"sequence":[63,148],"PBs.":[65],"simple":[68],"Needleman-Wunsch":[69],"approach":[70,93],"raw":[73],"PB":[74,97],"substitution":[75],"matrix,":[76],"PB-based":[77],"alignments":[79,114,118],"were":[80,119],"better":[81,121],"than":[82,122],"many":[83],"popular":[84],"methods.":[85],"iPBA":[86,117,191],"web":[87],"server":[88],"presents":[89],"improved":[91],"alignment":[92,104,149,161],"using":[94,155],"(i)":[95],"specialized":[96],"Substitution":[98],"Matrices":[99],"(SM)":[100],"(ii)":[102],"anchor-based":[103],"methodology.":[105],"these":[107],"developments,":[108],"quality":[110],"\u223c88%":[112],"was":[115],"improved.":[116],"also":[120,168],"DALI,":[123],"MUSTANG":[124],"GANGSTA(+)":[126],">80%":[128],"cases.":[131],"The":[132],"webserver":[133],"designed":[135],"to":[136,187],"both":[138],"pairwise":[139],"comparisons":[140],"database":[142],"searches.":[143],"Outputs":[144],"are":[145],"given":[146],"as":[147],"superposed":[151],"structures":[153],"displayed":[154],"PyMol":[156],"Jmol.":[158],"A":[159],"local":[160],"option":[162],"detecting":[164],"subs-structural":[165],"similarity":[166],"embedded.":[169],"As":[170],"'sequence-based'":[175],"tool,":[178],"we":[179],"believe":[180],"it":[182],"will":[183],"quite":[185],"useful":[186],"scientific":[189],"community.":[190],"accessed":[194],"at":[195],"http://www.dsimb.inserm.fr/dsimb_tools/ipba/.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":8}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
