{"id":"https://openalex.org/W4391953704","doi":"https://doi.org/10.1371/journal.pcbi.1011812","title":"Inference of annealed protein fitness landscapes with AnnealDCA","display_name":"Inference of annealed protein fitness landscapes with AnnealDCA","publication_year":2024,"publication_date":"2024-02-20","ids":{"openalex":"https://openalex.org/W4391953704","doi":"https://doi.org/10.1371/journal.pcbi.1011812","pmid":"https://pubmed.ncbi.nlm.nih.gov/38377054"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011812","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011812","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011812&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011812&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082007591","display_name":"Luca Sesta","orcid":"https://orcid.org/0000-0002-6051-0972"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Luca Sesta","raw_affiliation_strings":["Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011435835","display_name":"Andrea Pagnani","orcid":"https://orcid.org/0000-0002-6509-0807"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]},{"id":"https://openalex.org/I4210099850","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Torino","ror":"https://ror.org/01vj6ck58","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210099850"]},{"id":"https://openalex.org/I4210123319","display_name":"Italian institute for Genomic Medicine","ror":"https://ror.org/036054d36","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210123319"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Andrea Pagnani","raw_affiliation_strings":["Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy","INFN, Sezione di Torino, Torino, Italy","Italian Institute for Genomic Medicine, Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy","institution_ids":["https://openalex.org/I177477856"]},{"raw_affiliation_string":"INFN, Sezione di Torino, Torino, Italy","institution_ids":["https://openalex.org/I4210099850"]},{"raw_affiliation_string":"Italian Institute for Genomic Medicine, Torino, Italy","institution_ids":["https://openalex.org/I4210123319"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002616738","display_name":"Jorge Fern\u00e1ndez-de-Cossio-D\u00edaz","orcid":"https://orcid.org/0000-0002-4476-805X"},"institutions":[{"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/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210129651","display_name":"Laboratoire de Physique de l'Ecole Normale Sup\u00e9rieure","ror":"https://ror.org/03a26mh11","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I2746051580","https://openalex.org/I277688954","https://openalex.org/I29607241","https://openalex.org/I39804081","https://openalex.org/I4210129651","https://openalex.org/I4210148025","https://openalex.org/I4210148430"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Jorge Fernandez-de-Cossio-Diaz","raw_affiliation_strings":["Laboratory of Physics of the Ecole Normale Sup\u00e9rieure, CNRS UMR 8023 & PSL Research, Sorbonne Universit\u00e9, Paris, France"],"affiliations":[{"raw_affiliation_string":"Laboratory of Physics of the Ecole Normale Sup\u00e9rieure, CNRS UMR 8023 & PSL Research, Sorbonne Universit\u00e9, Paris, France","institution_ids":["https://openalex.org/I4210129651","https://openalex.org/I29607241","https://openalex.org/I1294671590","https://openalex.org/I39804081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086941438","display_name":"Guido Uguzzoni","orcid":"https://orcid.org/0000-0003-4192-2864"},"institutions":[{"id":"https://openalex.org/I4210123319","display_name":"Italian institute for Genomic Medicine","ror":"https://ror.org/036054d36","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210123319"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Guido Uguzzoni","raw_affiliation_strings":["Italian Institute for Genomic Medicine, Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Italian Institute for Genomic Medicine, Torino, Italy","institution_ids":["https://openalex.org/I4210123319"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5002616738","https://openalex.org/A5011435835","https://openalex.org/A5082007591","https://openalex.org/A5086941438"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I177477856","https://openalex.org/I29607241","https://openalex.org/I39804081","https://openalex.org/I4210099850","https://openalex.org/I4210123319","https://openalex.org/I4210129651"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.617,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.82948788,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"20","issue":"2","first_page":"e1011812","last_page":"e1011812"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9948999881744385,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9912999868392944,"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/inference","display_name":"Inference","score":0.6510095596313477},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6092624068260193},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5422400832176208},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4994018077850342},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.49027159810066223},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.4794011116027832},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45096921920776367},{"id":"https://openalex.org/keywords/disjoint-sets","display_name":"Disjoint sets","score":0.44960808753967285},{"id":"https://openalex.org/keywords/fitness-landscape","display_name":"Fitness landscape","score":0.437943696975708},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.404996395111084},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4005322754383087},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3530752658843994},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1809663474559784},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1272801160812378},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.11975264549255371},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08395013213157654}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6510095596313477},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6092624068260193},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5422400832176208},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4994018077850342},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.49027159810066223},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.4794011116027832},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45096921920776367},{"id":"https://openalex.org/C45340560","wikidata":"https://www.wikidata.org/wiki/Q215382","display_name":"Disjoint sets","level":2,"score":0.44960808753967285},{"id":"https://openalex.org/C91852762","wikidata":"https://www.wikidata.org/wiki/Q3307742","display_name":"Fitness landscape","level":3,"score":0.437943696975708},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.404996395111084},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4005322754383087},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3530752658843994},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1809663474559784},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1272801160812378},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.11975264549255371},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08395013213157654},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056084","descriptor_name":"Genetic Fitness","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056084","descriptor_name":"Genetic Fitness","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056084","descriptor_name":"Genetic Fitness","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011812","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011812","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011812&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:38377054","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38377054","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:HAL:hal-04733981v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04733981","pdf_url":"https://hal.science/hal-04733981/document","source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 2024, 20 (2), pp.e1011812. ⟨10.1371/journal.pcbi.1011812⟩","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:10878520","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10878520","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10878520/pdf/pcbi.1011812.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:748fac7a95b3481d9d0044122031bc14","is_oa":true,"landing_page_url":"https://doaj.org/article/748fac7a95b3481d9d0044122031bc14","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 2, p e1011812 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011812","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011812","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011812&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G5859239756","display_name":null,"funder_award_id":"MSCA-RISE","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G8886304095","display_name":null,"funder_award_id":"734439","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391953704.pdf","grobid_xml":"https://content.openalex.org/works/W4391953704.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1493541064","https://openalex.org/W1861406683","https://openalex.org/W1940255384","https://openalex.org/W1969012077","https://openalex.org/W1979762151","https://openalex.org/W1983416604","https://openalex.org/W1989901670","https://openalex.org/W2008545402","https://openalex.org/W2010053735","https://openalex.org/W2011343696","https://openalex.org/W2024060531","https://openalex.org/W2033765657","https://openalex.org/W2043484919","https://openalex.org/W2048310584","https://openalex.org/W2060588922","https://openalex.org/W2072010276","https://openalex.org/W2085144875","https://openalex.org/W2092572492","https://openalex.org/W2130710252","https://openalex.org/W2137566700","https://openalex.org/W2139365100","https://openalex.org/W2144893575","https://openalex.org/W2151887741","https://openalex.org/W2164814134","https://openalex.org/W2227467442","https://openalex.org/W2234497665","https://openalex.org/W2245592118","https://openalex.org/W2295956658","https://openalex.org/W2341538749","https://openalex.org/W2471654536","https://openalex.org/W2483469645","https://openalex.org/W2744336424","https://openalex.org/W2782613909","https://openalex.org/W2790509526","https://openalex.org/W2795578759","https://openalex.org/W2943267083","https://openalex.org/W2950118240","https://openalex.org/W2972671276","https://openalex.org/W2988868594","https://openalex.org/W2991119044","https://openalex.org/W2996272234","https://openalex.org/W2999957331","https://openalex.org/W3011455800","https://openalex.org/W3013072344","https://openalex.org/W3047799377","https://openalex.org/W3048714202","https://openalex.org/W3062028978","https://openalex.org/W3151229614","https://openalex.org/W3206320462","https://openalex.org/W3214001634","https://openalex.org/W4200219776","https://openalex.org/W4224317046","https://openalex.org/W4225384933","https://openalex.org/W4297990198","https://openalex.org/W4309306331","https://openalex.org/W4311235643","https://openalex.org/W4386529944","https://openalex.org/W4391732623"],"related_works":["https://openalex.org/W3129816939","https://openalex.org/W2912862995","https://openalex.org/W2985427592","https://openalex.org/W2101501829","https://openalex.org/W2400569965","https://openalex.org/W2060263731","https://openalex.org/W2003194288","https://openalex.org/W391093122","https://openalex.org/W4256429076","https://openalex.org/W2073086338"],"abstract_inverted_index":{"The":[0],"design":[1],"of":[2,36,92,107,117,126,143,149,158,170],"proteins":[3],"with":[4,14],"specific":[5],"tasks":[6],"is":[7],"a":[8,33,60,75,89,141],"major":[9],"challenge":[10],"in":[11,168],"molecular":[12],"biology":[13],"important":[15],"diagnostic":[16],"and":[17,97,120,151,162],"therapeutic":[18],"applications.":[19],"High-throughput":[20],"screening":[21,121],"methods":[22],"have":[23],"been":[24],"developed":[25],"to":[26,54,65,78,99,113,136],"systematically":[27],"evaluate":[28],"protein":[29,38,81,101,144],"activity,":[30],"but":[31],"only":[32],"small":[34],"fraction":[35],"possible":[37],"variants":[39,145,159],"can":[40,133,164],"be":[41,134,165],"tested":[42],"using":[43],"these":[44],"techniques.":[45],"Computational":[46],"models":[47],"that":[48,94],"explore":[49],"the":[50,56,80,105,124,127,156],"sequence":[51,172],"space":[52],"in-silico":[53],"identify":[55],"fittest":[57],"molecules":[58],"for":[59],"given":[61],"function":[62],"are":[63],"needed":[64],"overcome":[66],"this":[67,70],"limitation.":[68],"In":[69],"article,":[71],"we":[72],"propose":[73],"AnnealDCA,":[74],"machine-learning":[76],"framework":[77],"learn":[79],"fitness":[82,128],"landscape":[83,129],"from":[84,88],"sequencing":[85,98],"data":[86,116],"derived":[87],"broad":[90],"range":[91],"experiments":[93],"use":[95],"selection":[96,150],"quantify":[100],"activity.":[102],"We":[103],"demonstrate":[104],"effectiveness":[106],"our":[108],"method":[109,132],"by":[110],"applying":[111],"it":[112],"antibody":[114],"Rep-Seq":[115],"immunized":[118],"mice":[119],"experiments,":[122],"assessing":[123],"quality":[125],"reconstructions.":[130],"Our":[131],"applied":[135],"several":[137],"experimental":[138],"cases":[139,169],"where":[140],"population":[142],"undergoes":[146],"various":[147],"rounds":[148],"sequencing,":[152],"without":[153],"relying":[154],"on":[155],"computation":[157],"enrichment":[160],"ratios,":[161],"thus":[163],"used":[166],"even":[167],"disjoint":[171],"samples.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}