{"id":"https://openalex.org/W4388486442","doi":"https://doi.org/10.1093/bioinformatics/btad671","title":"PROSTATA: a framework for protein stability assessment using transformers","display_name":"PROSTATA: a framework for protein stability assessment using transformers","publication_year":2023,"publication_date":"2023-11-01","ids":{"openalex":"https://openalex.org/W4388486442","doi":"https://doi.org/10.1093/bioinformatics/btad671","pmid":"https://pubmed.ncbi.nlm.nih.gov/37935419"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad671","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad671","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad671/52812023/btad671.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/btad671/52812023/btad671.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044177617","display_name":"Dmitriy Umerenkov","orcid":"https://orcid.org/0000-0003-0413-7170"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Dmitriy Umerenkov","raw_affiliation_strings":["Sber AI Lab , Moscow 105064, Russia"],"affiliations":[{"raw_affiliation_string":"Sber AI Lab , Moscow 105064, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003964555","display_name":"Fedor Nikolaev","orcid":"https://orcid.org/0000-0001-6343-1623"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fedor Nikolaev","raw_affiliation_strings":["Bioinformatics Group, AIRI , Moscow 121170, Russia"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, AIRI , Moscow 121170, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020182590","display_name":"Tatiana Shashkova","orcid":"https://orcid.org/0000-0002-8754-8727"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tatiana I Shashkova","raw_affiliation_strings":["Bioinformatics Group, AIRI , Moscow 121170, Russia"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, AIRI , Moscow 121170, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016512248","display_name":"\u041f. \u0412. \u0421\u0442\u0440\u0430\u0448\u043d\u043e\u0432","orcid":"https://orcid.org/0000-0001-5001-146X"},"institutions":[{"id":"https://openalex.org/I177537411","display_name":"Bauman Moscow State Technical University","ror":"https://ror.org/00pb8h375","country_code":"RU","type":"education","lineage":["https://openalex.org/I177537411"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Pavel V Strashnov","raw_affiliation_strings":["Bioinformatics Group, AIRI , Moscow 121170, Russia","Department of Computer Design and Technology, Bauman Moscow State Technical University , Moscow 105005, Russia"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, AIRI , Moscow 121170, Russia","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Design and Technology, Bauman Moscow State Technical University , Moscow 105005, Russia","institution_ids":["https://openalex.org/I177537411"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073407846","display_name":"Maria Sindeeva","orcid":"https://orcid.org/0000-0002-1629-7756"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maria Sindeeva","raw_affiliation_strings":["Bioinformatics Group, AIRI , Moscow 121170, Russia"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, AIRI , Moscow 121170, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043625670","display_name":"Andrey Shevtsov","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Andrey Shevtsov","raw_affiliation_strings":["Bioinformatics Group, AIRI , Moscow 121170, Russia","Regulatory Transcriptomics and Epigenomics Group, Institute of Bioengineering, Research Center of Biotechnology RAS , Moscow 117036, Russia"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, AIRI , Moscow 121170, Russia","institution_ids":[]},{"raw_affiliation_string":"Regulatory Transcriptomics and Epigenomics Group, Institute of Bioengineering, Research Center of Biotechnology RAS , Moscow 117036, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076841276","display_name":"Nikita V. Ivanisenko","orcid":"https://orcid.org/0000-0002-0333-8117"},"institutions":[{"id":"https://openalex.org/I4210127387","display_name":"Siberian Branch of the Russian Academy of Sciences","ror":"https://ror.org/02frkq021","country_code":"RU","type":"funder","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210127387"]},{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Nikita V Ivanisenko","raw_affiliation_strings":["Bioinformatics Group, AIRI , Moscow 121170, Russia","Laboratory of Computational Proteomics, Institute of Cytology and Genetics SB RAS , Novosibirsk 630090, Russia","Laboratory of Computational Proteomics, Institute of Cytology and Genetics SB RAS, Lavrentyeva Avenue, 10, 630090, Novosibirsk, Russia"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, AIRI , Moscow 121170, Russia","institution_ids":[]},{"raw_affiliation_string":"Laboratory of Computational Proteomics, Institute of Cytology and Genetics SB RAS , Novosibirsk 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]},{"raw_affiliation_string":"Laboratory of Computational Proteomics, Institute of Cytology and Genetics SB RAS, Lavrentyeva Avenue, 10, 630090, Novosibirsk, Russia","institution_ids":["https://openalex.org/I4210116466","https://openalex.org/I4210127387"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028345035","display_name":"Olga Kardymon","orcid":"https://orcid.org/0000-0002-4827-8891"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Olga L Kardymon","raw_affiliation_strings":["Bioinformatics Group, AIRI , Moscow 121170, Russia"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, AIRI , Moscow 121170, Russia","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5044177617"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.5945,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.96880885,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"39","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9876999855041504,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9876999855041504,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9839000105857849,"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":0.9724000096321106,"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/computer-science","display_name":"Computer science","score":0.7887682914733887},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.631650447845459},{"id":"https://openalex.org/keywords/margin","display_name":"Margin (machine learning)","score":0.5664066672325134},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5140682458877563},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4649900794029236},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.46251359581947327},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.42840737104415894},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.41078561544418335},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35965797305107117},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07403582334518433},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.06809797883033752}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7887682914733887},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.631650447845459},{"id":"https://openalex.org/C774472","wikidata":"https://www.wikidata.org/wiki/Q6760393","display_name":"Margin (machine learning)","level":2,"score":0.5664066672325134},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5140682458877563},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4649900794029236},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.46251359581947327},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.42840737104415894},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.41078561544418335},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35965797305107117},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07403582334518433},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.06809797883033752},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad671","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad671","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad671/52812023/btad671.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:37935419","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37935419","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:10651431","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10651431","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10651431/pdf/btad671.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad671","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad671","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad671/52812023/btad671.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":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.46000000834465027}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4388486442.pdf"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W2008708467","https://openalex.org/W2031553026","https://openalex.org/W2051210555","https://openalex.org/W2064488723","https://openalex.org/W2102461176","https://openalex.org/W2142678478","https://openalex.org/W2149580316","https://openalex.org/W2151529283","https://openalex.org/W2153457180","https://openalex.org/W2324374958","https://openalex.org/W2335773464","https://openalex.org/W2428593791","https://openalex.org/W2557595285","https://openalex.org/W2606439133","https://openalex.org/W2615841538","https://openalex.org/W2793168264","https://openalex.org/W2794503008","https://openalex.org/W2801491392","https://openalex.org/W2896457183","https://openalex.org/W2912783011","https://openalex.org/W2944245644","https://openalex.org/W2955704392","https://openalex.org/W2998716839","https://openalex.org/W3012929814","https://openalex.org/W3083008290","https://openalex.org/W3105751341","https://openalex.org/W3109312535","https://openalex.org/W3117622225","https://openalex.org/W3136963718","https://openalex.org/W3156303331","https://openalex.org/W3171084190","https://openalex.org/W3171481040","https://openalex.org/W3177828909","https://openalex.org/W4205480045","https://openalex.org/W4206007286","https://openalex.org/W4210494137","https://openalex.org/W4225930681","https://openalex.org/W4229331784","https://openalex.org/W4288068292","https://openalex.org/W4292002633","https://openalex.org/W4295929073","https://openalex.org/W4304480239","https://openalex.org/W4327550249","https://openalex.org/W4362664882","https://openalex.org/W4366392978","https://openalex.org/W4379600237","https://openalex.org/W4384820649","https://openalex.org/W4386154677"],"related_works":["https://openalex.org/W3125011624","https://openalex.org/W1508631387","https://openalex.org/W2370917603","https://openalex.org/W2952760143","https://openalex.org/W2017776670","https://openalex.org/W2347897961","https://openalex.org/W2979236518","https://openalex.org/W2358318464","https://openalex.org/W2340870721","https://openalex.org/W3091955004"],"abstract_inverted_index":{"PROSTATA":[0],"is":[1],"available":[2],"at":[3],"https://github.com/AIRI-Institute/PROSTATA":[4],"and":[5],"https://prostata.airi.net.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":1}],"updated_date":"2026-01-25T23:04:38.658462","created_date":"2025-10-10T00:00:00"}
