{"id":"https://openalex.org/W2005240848","doi":"https://doi.org/10.1186/1471-2105-11-75","title":"Mining protein loops using a structural alphabet and statistical exceptionality","display_name":"Mining protein loops using a structural alphabet and statistical exceptionality","publication_year":2010,"publication_date":"2010-02-04","ids":{"openalex":"https://openalex.org/W2005240848","doi":"https://doi.org/10.1186/1471-2105-11-75","mag":"2005240848","pmid":"https://pubmed.ncbi.nlm.nih.gov/20132552"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-75","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-75","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-75","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-75","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066913640","display_name":"Leslie Regad","orcid":"https://orcid.org/0000-0002-9292-5283"},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"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"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Leslie Regad","raw_affiliation_strings":["MTi, Inserm UMR-S 973, Universit\u00e9 Paris Diderot- Paris 7, Paris, F-75205 Cedex 13, France. leslie.regad@univ-paris-diderot.fr","MTi, Inserm UMR-S 973, Universit\u00e9 Paris Diderot- Paris 7, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MTi, Inserm UMR-S 973, Universit\u00e9 Paris Diderot- Paris 7, Paris, F-75205 Cedex 13, France. leslie.regad@univ-paris-diderot.fr","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I169173203","https://openalex.org/I204730241"]},{"raw_affiliation_string":"MTi, Inserm UMR-S 973, Universit\u00e9 Paris Diderot- Paris 7, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I169173203","https://openalex.org/I204730241"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026973395","display_name":"Juliette Martin","orcid":"https://orcid.org/0000-0002-4787-0885"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210087293","display_name":"Institut de Biologie et de Chimie des Prot\u00e9ines","ror":"https://ror.org/0019x5d05","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I4210087293","https://openalex.org/I4210096427"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Juliette Martin","raw_affiliation_strings":["IFR 128, CNRS, UMR 5086, IBCP, Institut de Biologie et Chimie des Prot\u00e9ines, Universit\u00e9 Lyon 1, Lyon, F-69367, France","Unite Math\u00e9matiques Informatique et G\u00e9nome UR1077, INRA, Jouy-en-Josas, F-78350, France","IFR 128, CNRS, UMR 5086, IBCP, Institut de Biologie et Chimie des Prot\u00e9ines, Universit\u00e9 Lyon 1, Lyon, France","Unite Math\u00e9matiques Informatique et G\u00e9nome UR1077, INRA, Jouy-en-Josas, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IFR 128, CNRS, UMR 5086, IBCP, Institut de Biologie et Chimie des Prot\u00e9ines, Universit\u00e9 Lyon 1, Lyon, F-69367, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I4210087293"]},{"raw_affiliation_string":"Unite Math\u00e9matiques Informatique et G\u00e9nome UR1077, INRA, Jouy-en-Josas, F-78350, France","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"IFR 128, CNRS, UMR 5086, IBCP, Institut de Biologie et Chimie des Prot\u00e9ines, Universit\u00e9 Lyon 1, Lyon, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I4210087293"]},{"raw_affiliation_string":"Unite Math\u00e9matiques Informatique et G\u00e9nome UR1077, INRA, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109225913","display_name":"Gr\u00e9gory Nuel","orcid":null},"institutions":[{"id":"https://openalex.org/I110736937","display_name":"D\u00e9l\u00e9gation Paris 5","ror":"https://ror.org/02e0y6e06","country_code":"FR","type":"government","lineage":["https://openalex.org/I110736937","https://openalex.org/I154526488"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"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/I4387154995","display_name":"Math\u00e9matiques Appliqu\u00e9es \u00e0 Paris 5","ror":"https://ror.org/04yrrdj53","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4387154995"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Gregory Nuel","raw_affiliation_strings":["MAP5, UMR CNRS 8145, Universit\u00e9 Paris-Descartes, Paris, F-75006, France","MAP5, UMR CNRS 8145, Universit\u00e9 Paris Descartes, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MAP5, UMR CNRS 8145, Universit\u00e9 Paris-Descartes, Paris, F-75006, France","institution_ids":["https://openalex.org/I110736937","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4387154995"]},{"raw_affiliation_string":"MAP5, UMR CNRS 8145, Universit\u00e9 Paris Descartes, Paris, France","institution_ids":["https://openalex.org/I110736937","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4387154995"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015097541","display_name":"Anne\u2010Claude Camproux","orcid":"https://orcid.org/0000-0001-8821-9952"},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"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"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anne-Claude Camproux","raw_affiliation_strings":["MTi, Inserm UMR-S 973, Universit\u00e9 Paris Diderot- Paris 7, Paris, F-75205 Cedex 13, France","MTi, Inserm UMR-S 973, Universit\u00e9 Paris Diderot- Paris 7, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MTi, Inserm UMR-S 973, Universit\u00e9 Paris Diderot- Paris 7, Paris, F-75205 Cedex 13, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I169173203","https://openalex.org/I204730241"]},{"raw_affiliation_string":"MTi, Inserm UMR-S 973, Universit\u00e9 Paris Diderot- Paris 7, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I169173203","https://openalex.org/I204730241"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5066913640"],"corresponding_institution_ids":["https://openalex.org/I154526488","https://openalex.org/I169173203","https://openalex.org/I204730241"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.6187,"has_fulltext":true,"cited_by_count":37,"citation_normalized_percentile":{"value":0.82153947,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"11","issue":"1","first_page":"75","last_page":"75"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.4934000074863434,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.4934000074863434,"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":0.06239999830722809,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.05990000069141388,"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/loop-modeling","display_name":"Loop modeling","score":0.7864574193954468},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.6236685514450073},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5786690711975098},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5712682008743286},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.533699631690979},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5159772038459778},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.5024008750915527},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.48623624444007874},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.476762592792511},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.47195306420326233},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.4492895305156708},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40375810861587524},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.34644240140914917},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.3052665591239929},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25876182317733765},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24219441413879395},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2225070595741272},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2013305127620697},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.19751885533332825},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.18628132343292236},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.16494184732437134}],"concepts":[{"id":"https://openalex.org/C45475804","wikidata":"https://www.wikidata.org/wiki/Q6675846","display_name":"Loop modeling","level":4,"score":0.7864574193954468},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.6236685514450073},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5786690711975098},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5712682008743286},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.533699631690979},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5159772038459778},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.5024008750915527},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.48623624444007874},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.476762592792511},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47195306420326233},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.4492895305156708},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40375810861587524},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.34644240140914917},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.3052665591239929},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25876182317733765},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24219441413879395},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2225070595741272},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2013305127620697},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.19751885533332825},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.18628132343292236},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.16494184732437134},{"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","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":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-11-75","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-75","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-75","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20132552","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20132552","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2833150","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2833150","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:HAL:inserm-00656194v1","is_oa":true,"landing_page_url":"https://inserm.hal.science/inserm-00656194","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":"BMC Bioinformatics, 2010, 11 (1), pp.75. &#x27E8;10.1186/1471-2105-11-75&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:170bc18d486543699a81ba9a23ae5295","is_oa":false,"landing_page_url":"https://doaj.org/article/170bc18d486543699a81ba9a23ae5295","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 75 (2010)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-75","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-75","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-75","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323910","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/01x3gbx83"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2005240848.pdf","grobid_xml":"https://content.openalex.org/works/W2005240848.grobid-xml"},"referenced_works_count":83,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1470225921","https://openalex.org/W1482207933","https://openalex.org/W1495099700","https://openalex.org/W1519235666","https://openalex.org/W1586022877","https://openalex.org/W1592824476","https://openalex.org/W1600771042","https://openalex.org/W1605897306","https://openalex.org/W1678387880","https://openalex.org/W1915528038","https://openalex.org/W1965555277","https://openalex.org/W1970654380","https://openalex.org/W1971099088","https://openalex.org/W1985744441","https://openalex.org/W2004234681","https://openalex.org/W2007048003","https://openalex.org/W2008708467","https://openalex.org/W2012702817","https://openalex.org/W2014270184","https://openalex.org/W2015976911","https://openalex.org/W2016483318","https://openalex.org/W2018461502","https://openalex.org/W2019572077","https://openalex.org/W2021197145","https://openalex.org/W2025822492","https://openalex.org/W2025932643","https://openalex.org/W2032643862","https://openalex.org/W2038147123","https://openalex.org/W2040273327","https://openalex.org/W2043078269","https://openalex.org/W2044284701","https://openalex.org/W2049821875","https://openalex.org/W2050085817","https://openalex.org/W2050322157","https://openalex.org/W2058693233","https://openalex.org/W2059120410","https://openalex.org/W2059203643","https://openalex.org/W2060418270","https://openalex.org/W2060459182","https://openalex.org/W2065509725","https://openalex.org/W2067816758","https://openalex.org/W2069319961","https://openalex.org/W2072138955","https://openalex.org/W2072287929","https://openalex.org/W2073032874","https://openalex.org/W2074655761","https://openalex.org/W2075820422","https://openalex.org/W2081516433","https://openalex.org/W2082535576","https://openalex.org/W2088082060","https://openalex.org/W2092036496","https://openalex.org/W2096425628","https://openalex.org/W2101386484","https://openalex.org/W2103612114","https://openalex.org/W2106976556","https://openalex.org/W2107966552","https://openalex.org/W2111329690","https://openalex.org/W2111696858","https://openalex.org/W2113403117","https://openalex.org/W2125800162","https://openalex.org/W2125838338","https://openalex.org/W2134312057","https://openalex.org/W2136517237","https://openalex.org/W2137760272","https://openalex.org/W2146231163","https://openalex.org/W2148757883","https://openalex.org/W2149943853","https://openalex.org/W2152655599","https://openalex.org/W2154588369","https://openalex.org/W2155063211","https://openalex.org/W2156367275","https://openalex.org/W2157485293","https://openalex.org/W2162219170","https://openalex.org/W2170535845","https://openalex.org/W2171172158","https://openalex.org/W2225480587","https://openalex.org/W2477521491","https://openalex.org/W2797579686","https://openalex.org/W2973456924","https://openalex.org/W3109965631","https://openalex.org/W4296472334","https://openalex.org/W4301258660"],"related_works":["https://openalex.org/W2607853144","https://openalex.org/W2099254366","https://openalex.org/W2121688928","https://openalex.org/W2969133412","https://openalex.org/W1997379747","https://openalex.org/W2084743099","https://openalex.org/W2125800162","https://openalex.org/W2005240848","https://openalex.org/W2106883599","https://openalex.org/W4232453105"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"loops":[2,30,70,97,179,198,224,310,379,442],"encompass":[3],"50%":[4],"of":[5,28,57,90,93,119,128,144,148,176,197,199,208,223,235,247,260,266,290,297,308,324,328,340,349,450],"protein":[6,18,29,122,164,178,378,433,441],"residues":[7,210],"in":[8,17,55,162,173,332,409,432],"available":[9,456],"three-dimensional":[10,121],"structures.":[11],"These":[12,251],"regions":[13],"are":[14,52,61,237,277,343,407,455],"often":[15],"involved":[16],"functions,":[19],"e.g.":[20],"binding":[21],"site,":[22],"catalytic":[23],"pocket...":[24],"However,":[25],"the":[26,86,91,111,117,145,185,205,217,322,389,420,429,448],"description":[27,87],"with":[31,300,321],"conventional":[32,163,333],"tools":[33],"is":[34,108,133,152,386,419],"an":[35],"uneasy":[36],"task.":[37],"Regular":[38],"secondary":[39],"structures,":[40],"helices":[41],"and":[42,59,81,88,95,180,285,306,345,359,376,393,398,412,443],"strands,":[43],"have":[44,71,254],"been":[45,73],"widely":[46],"studied":[47],"whereas":[48],"loops,":[49],"because":[50],"they":[51],"highly":[53,220,242],"variable":[54],"terms":[56],"sequence":[58,165,335],"structure,":[60],"difficult":[62,142],"to":[63,66,184,373,427,438,446],"analyze.":[64],"Due":[65],"data":[67,150],"sparsity,":[68],"long":[69,96,286,309,413],"rarely":[72],"systematically":[74,168,374],"studied.":[75],"RESULTS:":[76],"We":[77,167,215,317,369,401],"developed":[78,370],"a":[79,120,125,134,174,194,270,294,371],"simple":[80],"accurate":[82],"method":[83,107,372,385],"that":[84,233,406,423],"allows":[85,116],"analysis":[89,196,218,320],"structures":[92],"short":[94,280,411],"using":[98,380],"structural":[99,112,139,146,158,189,206,244,252,256,329,341,357,364,382,390,396,404],"motifs":[100,207,268,292,405],"without":[101],"restriction":[102],"on":[103,110,219,388,395],"loop":[104,350],"length.":[105],"This":[106,191,384,435],"based":[109,387],"alphabet":[113,391],"HMM-SA.":[114],"HMM-SA":[115,392],"simplification":[118],"structure":[123],"into":[124],"one-dimensional":[126],"string":[127],"states,":[129],"where":[130],"each":[131],"state":[132],"four-residue":[135],"prototype":[136],"fragment,":[137],"called":[138],"letter.":[140],"The":[141],"task":[143],"grouping":[147],"huge":[149],"sets":[151],"thus":[153],"easily":[154],"accomplished":[155],"by":[156,239,279],"handling":[157],"letter":[159],"strings":[160],"as":[161,331],"analysis.":[166,336,452],"extracted":[169,402],"all":[170,200],"seven-residue":[171],"fragments":[172],"bank":[175],"93000":[177],"grouped":[181],"them":[182],"according":[183],"structural-letter":[186],"sequence,":[187],"named":[188],"word.":[190,316],"approach":[192],"permits":[193],"systematic":[195],"sizes":[201],"since":[202],"we":[203],"consider":[204],"seven":[209],"rather":[211],"than":[212,227,282],"complete":[213],"loops.":[214,287,414,434],"focused":[216],"recurrent":[221,243,291,381],"words":[222,245,253,342,354],"(observed":[225],"more":[226],"30":[228],"times).":[229],"Our":[230],"study":[231,377],"reveals":[232],"73%":[234],"loop-lengths":[236],"covered":[238],"only":[240],"3310":[241],"out":[246],"28274":[248],"observed":[249],"words).":[250],"low":[255],"variability":[257,358],"(mean":[258],"RMSd":[259],"0.85":[261],"A).":[262],"As":[263],"expected,":[264],"half":[265,289],"these":[267,353],"display":[269],"flanking-region":[271],"preference":[272],"but":[273],"interestingly,":[274],"two":[275],"thirds":[276],"shared":[278],"(less":[281],"12":[283],"residues)":[284],"Moreover,":[288],"exhibit":[293,355],"significant":[295,304],"level":[296],"amino-acid":[298],"conservation":[299],"at":[301,312,457],"least":[302,313],"four":[303],"positions":[305],"87%":[307],"contain":[311],"one":[314],"such":[315],"complement":[318],"our":[319,416],"detection":[323],"statistically":[325],"over-represented":[326],"patterns":[327],"letters":[330],"DNA":[334],"About":[337],"30%":[338],"(930)":[339],"over-represented,":[344],"cover":[346],"about":[347],"40%":[348],"lengths.":[351],"Interestingly,":[352],"lower":[356],"higher":[360],"sequential":[361],"specificity,":[362],"suggesting":[363],"or":[365],"functional":[366],"constraints.":[367],"CONCLUSIONS:":[368],"decompose":[375],"motifs.":[383],"not":[394],"alignment":[397],"geometrical":[399],"parameters.":[400],"meaningful":[403],"found":[408],"both":[410],"To":[415],"knowledge,":[417],"it":[418],"first":[421],"time":[422],"pattern":[424],"mining":[425],"helps":[426,437],"increase":[428],"signal-to-noise":[430],"ratio":[431],"finding":[436],"better":[439],"describe":[440],"might":[444],"permit":[445],"decrease":[447],"complexity":[449],"long-loop":[451],"Detailed":[453],"results":[454],"http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.":[458]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
