{"id":"https://openalex.org/W4409387561","doi":"https://doi.org/10.1093/bioinformatics/btaf166","title":"CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure","display_name":"CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure","publication_year":2025,"publication_date":"2025-03-29","ids":{"openalex":"https://openalex.org/W4409387561","doi":"https://doi.org/10.1093/bioinformatics/btaf166","pmid":"https://pubmed.ncbi.nlm.nih.gov/40220324"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf166","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf166","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf166/62922544/btaf166.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf166/62922544/btaf166.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109024868","display_name":"Lucas Chivot","orcid":null},"institutions":[{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Lucas Chivot","raw_affiliation_strings":["Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","institution_ids":["https://openalex.org/I62396329"]},{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,","institution_ids":["https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117121255","display_name":"No\u00e9 Mathieux","orcid":null},"institutions":[{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"No\u00e9 Mathieux","raw_affiliation_strings":["Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","institution_ids":["https://openalex.org/I62396329"]},{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,","institution_ids":["https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117121256","display_name":"Anna Cosson","orcid":null},"institutions":[{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anna Cosson","raw_affiliation_strings":["Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","institution_ids":["https://openalex.org/I62396329"]},{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,","institution_ids":["https://openalex.org/I62396329"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045887676","display_name":"Antoine Bridier\u2010Nahmias","orcid":"https://orcid.org/0000-0002-0376-6840"},"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/I4210091279","display_name":"Universit\u00e9 Sorbonne Paris Nord","ror":"https://ror.org/0199hds37","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210091279"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4387156044","display_name":"Infection, Anti-microbiens, Mod\u00e9lisation, Evolution","ror":"https://ror.org/05hqep952","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4387156044"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Antoine Bridier-Nahmias","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9 et Sorbonne Paris Nord, Inserm, IAME , F-75018 Paris,","Universit\u00e9 Paris Cit\u00e9 et Sorbonne Paris Nord , Inserm, IAME, Paris,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9 et Sorbonne Paris Nord, Inserm, IAME , F-75018 Paris,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210091279","https://openalex.org/I4210091437","https://openalex.org/I4387156044"]},{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9 et Sorbonne Paris Nord , Inserm, IAME, Paris,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210091279","https://openalex.org/I4210091437","https://openalex.org/I4387156044"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033604967","display_name":"Lo\u00efc Favennec","orcid":"https://orcid.org/0000-0003-3386-2240"},"institutions":[{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Lo\u00efc Favennec","raw_affiliation_strings":["Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","institution_ids":["https://openalex.org/I62396329"]},{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,","institution_ids":["https://openalex.org/I62396329"]}]},{"author_position":"middle","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/I24715933","display_name":"University of Reunion Island","ror":"https://ror.org/005ypkf75","country_code":"RE","type":"education","lineage":["https://openalex.org/I24715933"]}],"countries":["FR","RE"],"is_corresponding":false,"raw_author_name":"Jean-Christophe Gelly","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9 et Universit\u00e9 des Antilles et Universit\u00e9 de la R\u00e9union, Inserm, BIGR , F-75015 Paris,","Universit\u00e9 Paris Cit\u00e9 et Universit\u00e9 des Antilles et Universit\u00e9 de la R\u00e9union , Inserm, BIGR, Paris,"],"raw_orcid":"https://orcid.org/0000-0001-5138-361X","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9 et Universit\u00e9 des Antilles et Universit\u00e9 de la R\u00e9union, Inserm, BIGR , F-75015 Paris,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I24715933"]},{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9 et Universit\u00e9 des Antilles et Universit\u00e9 de la R\u00e9union , Inserm, BIGR, Paris,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071461810","display_name":"J\u00e9r\u00f4me Clain","orcid":"https://orcid.org/0000-0002-0232-5058"},"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/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210093064","display_name":"Sant\u00e9 Internationale de la m\u00e8re et de l'enfant","ror":"https://ror.org/00rd22143","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I204730241","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210093064","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"J\u00e9r\u00f4me Clain","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9, IRD, Inserm, MERIT , F-75006 Paris,","Universit\u00e9 Paris Cit\u00e9, IRD, Inserm , MERIT, Paris,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, IRD, Inserm, MERIT , F-75006 Paris,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210091437","https://openalex.org/I4210166444"]},{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, IRD, Inserm , MERIT, Paris,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210093064","https://openalex.org/I4210166444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040657129","display_name":"Romain Copp\u00e9e","orcid":"https://orcid.org/0000-0002-3024-5928"},"institutions":[{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Romain Copp\u00e9e","raw_affiliation_strings":["Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,"],"raw_orcid":"https://orcid.org/0000-0002-3024-5928","affiliations":[{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, ESCAPE , F-76000 Rouen,","institution_ids":["https://openalex.org/I62396329"]},{"raw_affiliation_string":"Universit\u00e9 de Rouen Normandie, Laboratoire de Parasitologie-Mycologie , ESCAPE, Rouen,","institution_ids":["https://openalex.org/I62396329"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5040657129"],"corresponding_institution_ids":["https://openalex.org/I62396329"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2221,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.76784631,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"41","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9251999855041504,"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":0.9251999855041504,"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":0.03929999843239784,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00570000009611249,"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/construct","display_name":"Construct (python library)","score":0.8048617839813232},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6410471796989441},{"id":"https://openalex.org/keywords/protein-tertiary-structure","display_name":"Protein tertiary structure","score":0.5722478032112122},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4493834376335144},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43524807691574097},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3505503535270691},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25585752725601196},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08325791358947754}],"concepts":[{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.8048617839813232},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6410471796989441},{"id":"https://openalex.org/C75599170","wikidata":"https://www.wikidata.org/wiki/Q898483","display_name":"Protein tertiary structure","level":2,"score":0.5722478032112122},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4493834376335144},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43524807691574097},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3505503535270691},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25585752725601196},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08325791358947754}],"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf166","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf166","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf166/62922544/btaf166.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40220324","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40220324","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12034385","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12034385","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf166","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf166","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf166/62922544/btaf166.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6200000047683716,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409387561.pdf","grobid_xml":"https://content.openalex.org/works/W4409387561.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W598738849","https://openalex.org/W1588507374","https://openalex.org/W1864168052","https://openalex.org/W1967293793","https://openalex.org/W1974725200","https://openalex.org/W2000571781","https://openalex.org/W2002651564","https://openalex.org/W2003013893","https://openalex.org/W2013253738","https://openalex.org/W2027036222","https://openalex.org/W2040481795","https://openalex.org/W2043543538","https://openalex.org/W2054017637","https://openalex.org/W2064430199","https://openalex.org/W2077539484","https://openalex.org/W2110335151","https://openalex.org/W2113024639","https://openalex.org/W2116137622","https://openalex.org/W2122376908","https://openalex.org/W2124790653","https://openalex.org/W2137704498","https://openalex.org/W2142726203","https://openalex.org/W2146335990","https://openalex.org/W2147660889","https://openalex.org/W2154131901","https://openalex.org/W2160364329","https://openalex.org/W2160876388","https://openalex.org/W2162217690","https://openalex.org/W2163352757","https://openalex.org/W2266439690","https://openalex.org/W2397195294","https://openalex.org/W2768448654","https://openalex.org/W2900751195","https://openalex.org/W2951184823","https://openalex.org/W3005235420","https://openalex.org/W3081492719","https://openalex.org/W4229066198","https://openalex.org/W4353055525","https://openalex.org/W4378903186","https://openalex.org/W4391539546","https://openalex.org/W4396721167"],"related_works":["https://openalex.org/W2366107444","https://openalex.org/W4388145910","https://openalex.org/W2381570729","https://openalex.org/W1976205134","https://openalex.org/W4248336175","https://openalex.org/W2031260042","https://openalex.org/W2391445434","https://openalex.org/W3009369890","https://openalex.org/W4312490297","https://openalex.org/W2062212388"],"abstract_inverted_index":{"MOTIVATION:":[0],"Evolutionary":[1],"rates":[2,55,113,119,125],"in":[3,66,80,98],"protein-coding":[4],"genes":[5],"vary":[6],"widely,":[7],"reflecting":[8],"functional":[9,43,75,93],"and/or":[10,44],"structural":[11],"constraints.":[12],"Essential":[13],"or":[14,153],"highly":[15],"expressed":[16],"proteins":[17,175],"tend":[18,77],"to":[19,78],"evolve":[20],"more":[21],"slowly,":[22],"and":[23,58,94,169,182,214],"within":[24,131],"a":[25,103,195],"protein,":[26],"different":[27],"amino":[28,47,128,159],"acid":[29,48,129,160],"sites":[30,76,130],"experience":[31],"distinct":[32],"selective":[33],"pressures.":[34],"Accurately":[35],"modeling":[36],"this":[37],"variation":[38],"is":[39,71],"critical":[40],"for":[41,91,163,198],"identifying":[42],"structurally":[45,95],"important":[46,96],"sites.":[49],"Standard":[50],"methods":[51],"assume":[52],"independent":[53],"substitution":[54,112],"across":[56],"sites,":[57,161],"the":[59,115,124,139,154,186],"most":[60],"conserved":[61],"ones":[62],"are":[63,120,216],"widely":[64],"distributed":[65],"protein":[67,99,206],"tertiary":[68,100],"structure.":[69,101],"This":[70],"biologically":[72],"unrealistic,":[73],"as":[74,194],"cluster":[79],"3D":[81],"space.":[82],"RESULTS:":[83],"Here,":[84],"we":[85],"developed":[86],"CONSTRUCT,":[87],"an":[88,132],"improved":[89],"strategy":[90],"detecting":[92],"regions":[97],"Given":[102],"set":[104],"of":[105,126,156,158,176,188],"orthologous":[106],"sequences,":[107],"CONSTRUCT":[108,147,193,212],"first":[109],"estimates":[110],"site-specific":[111],"using":[114],"Rate4site":[116],"model.":[117],"These":[118],"then":[121],"weighted":[122],"by":[123,138],"neighboring":[127],"optimally":[133],"defined":[134],"window":[135],"size,":[136],"determined":[137],"strongest":[140],"spatial":[141],"correlation.":[142],"To":[143],"refine":[144],"clustering":[145],"detection,":[146],"can":[148],"analyze":[149],"either":[150],"C\u03b1":[151],"atoms":[152],"center":[155],"mass":[157],"accounting":[162],"side":[164],"chain":[165],"orientation.":[166],"Extensive":[167],"simulations":[168],"validation":[170],"on":[171],"14":[172],"functionally":[173],"characterized":[174],"diverse":[177],"sizes,":[178],"interspecies":[179],"conservation":[180],"levels,":[181],"taxonomic":[183],"origins":[184],"demonstrated":[185],"robustness":[187],"CONSTRUCT.":[189],"The":[190,211],"results":[191],"highlight":[192],"powerful":[196],"tool":[197],"guiding":[199],"site-directed":[200],"mutagenesis":[201],"experiments":[202],"aimed":[203],"at":[204,219],"elucidating":[205],"function.":[207],"AVAILABILITY":[208],"AND":[209],"IMPLEMENTATION:":[210],"program":[213],"documentation":[215],"freely":[217],"available":[218],"https://github.com/Rcoppee/CONSTRUCT.":[220]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
