{"id":"https://openalex.org/W2107029482","doi":"https://doi.org/10.1093/bioinformatics/btl218","title":"The iRMSD: a local measure of sequence alignment accuracy using structural information","display_name":"The iRMSD: a local measure of sequence alignment accuracy using structural information","publication_year":2006,"publication_date":"2006-07-15","ids":{"openalex":"https://openalex.org/W2107029482","doi":"https://doi.org/10.1093/bioinformatics/btl218","mag":"2107029482","pmid":"https://pubmed.ncbi.nlm.nih.gov/16873492"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl218","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl218","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e35/48841243/bioinformatics_22_14_e35.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e35/48841243/bioinformatics_22_14_e35.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052723939","display_name":"Fabrice Armougom","orcid":"https://orcid.org/0000-0003-0294-4913"},"institutions":[{"id":"https://openalex.org/I4387154720","display_name":"Laboratoire Information G\u00e9nomique et Structurale","ror":"https://ror.org/05v0fms67","country_code":null,"type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I21491767","https://openalex.org/I4387154720"]}],"countries":[],"is_corresponding":true,"raw_author_name":"Fabrice Armougom","raw_affiliation_strings":["Laboratoire Information G\u00e9nomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) 1 \u00a0 1 \u00a0 \u00a0 Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09"],"affiliations":[{"raw_affiliation_string":"Laboratoire Information G\u00e9nomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) 1 \u00a0 1 \u00a0 \u00a0 Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09","institution_ids":["https://openalex.org/I4387154720"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039131441","display_name":"S\u00e9bastien Moretti","orcid":"https://orcid.org/0000-0003-3947-488X"},"institutions":[{"id":"https://openalex.org/I4387154720","display_name":"Laboratoire Information G\u00e9nomique et Structurale","ror":"https://ror.org/05v0fms67","country_code":null,"type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I21491767","https://openalex.org/I4387154720"]}],"countries":[],"is_corresponding":false,"raw_author_name":"S\u00e9bastien Moretti","raw_affiliation_strings":["Laboratoire Information G\u00e9nomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) 1 \u00a0 1 \u00a0 \u00a0 Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09"],"affiliations":[{"raw_affiliation_string":"Laboratoire Information G\u00e9nomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) 1 \u00a0 1 \u00a0 \u00a0 Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09","institution_ids":["https://openalex.org/I4387154720"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026511052","display_name":"Vladimir Keduas","orcid":null},"institutions":[{"id":"https://openalex.org/I4387154720","display_name":"Laboratoire Information G\u00e9nomique et Structurale","ror":"https://ror.org/05v0fms67","country_code":null,"type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I21491767","https://openalex.org/I4387154720"]}],"countries":[],"is_corresponding":false,"raw_author_name":"Vladimir Keduas","raw_affiliation_strings":["Laboratoire Information G\u00e9nomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) 1 \u00a0 1 \u00a0 \u00a0 Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09"],"affiliations":[{"raw_affiliation_string":"Laboratoire Information G\u00e9nomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) 1 \u00a0 1 \u00a0 \u00a0 Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09","institution_ids":["https://openalex.org/I4387154720"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058332830","display_name":"C\u00e9dric Notredame","orcid":"https://orcid.org/0000-0003-1461-0988"},"institutions":[{"id":"https://openalex.org/I4387154720","display_name":"Laboratoire Information G\u00e9nomique et Structurale","ror":"https://ror.org/05v0fms67","country_code":null,"type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I21491767","https://openalex.org/I4387154720"]}],"countries":[],"is_corresponding":false,"raw_author_name":"Cedric Notredame","raw_affiliation_strings":["Laboratoire Information G\u00e9nomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) 1 \u00a0 1 \u00a0 \u00a0 Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09"],"affiliations":[{"raw_affiliation_string":"Laboratoire Information G\u00e9nomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) 1 \u00a0 1 \u00a0 \u00a0 Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09","institution_ids":["https://openalex.org/I4387154720"]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5052723939"],"corresponding_institution_ids":["https://openalex.org/I4387154720"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6252,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.82180285,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"14","first_page":"e35","last_page":"e39"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T11162","display_name":"Enzyme Structure and Function","score":0.996999979019165,"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":0.9952999949455261,"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":0.8029810786247253},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7830719947814941},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.6854267120361328},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6662943363189697},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6611865758895874},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5655286312103271},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5307008624076843},{"id":"https://openalex.org/keywords/superposition-principle","display_name":"Superposition principle","score":0.4443318843841553},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3968203067779541},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37208086252212524},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34259217977523804},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.20307958126068115},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20023643970489502},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1125122606754303},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07150280475616455}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.8029810786247253},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7830719947814941},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.6854267120361328},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6662943363189697},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6611865758895874},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5655286312103271},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5307008624076843},{"id":"https://openalex.org/C27753989","wikidata":"https://www.wikidata.org/wiki/Q284885","display_name":"Superposition principle","level":2,"score":0.4443318843841553},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3968203067779541},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37208086252212524},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34259217977523804},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.20307958126068115},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20023643970489502},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1125122606754303},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07150280475616455},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btl218","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl218","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e35/48841243/bioinformatics_22_14_e35.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16873492","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16873492","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl218","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl218","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e35/48841243/bioinformatics_22_14_e35.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G7758152977","display_name":null,"funder_award_id":"support","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"}],"funders":[{"id":"https://openalex.org/F4320307781","display_name":"Sanofi","ror":"https://ror.org/027vj4x92"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2107029482.pdf","grobid_xml":"https://content.openalex.org/works/W2107029482.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1567621547","https://openalex.org/W1968294149","https://openalex.org/W1986014242","https://openalex.org/W1987856282","https://openalex.org/W2004178884","https://openalex.org/W2022058405","https://openalex.org/W2077235131","https://openalex.org/W2102502076","https://openalex.org/W2106882534","https://openalex.org/W2118851904","https://openalex.org/W2127122014","https://openalex.org/W2132926880","https://openalex.org/W2136570298","https://openalex.org/W2137146016","https://openalex.org/W2140872496","https://openalex.org/W2143292980","https://openalex.org/W2144362290","https://openalex.org/W2147556320","https://openalex.org/W2152326664","https://openalex.org/W2157809793","https://openalex.org/W2169459078","https://openalex.org/W2187406058","https://openalex.org/W4244252686"],"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/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W187239587","https://openalex.org/W2141411672"],"abstract_inverted_index":{"The":[0],"iRMSD":[1],"is":[2,9],"part":[3],"of":[4],"the":[5],"T-Coffee":[6],"package":[7],"and":[8],"distributed":[10],"as":[11],"an":[12],"open":[13],"source":[14],"freeware":[15],"(http://www.tcoffee.org/).":[16]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-14T08:43:22.919905","created_date":"2025-10-10T00:00:00"}
