{"id":"https://openalex.org/W4410233685","doi":"https://doi.org/10.1093/bioinformatics/btaf270","title":"ProBASS\u2014a language model with sequence and structural features for predicting the effect of mutations on binding affinity","display_name":"ProBASS\u2014a language model with sequence and structural features for predicting the effect of mutations on binding affinity","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4410233685","doi":"https://doi.org/10.1093/bioinformatics/btaf270","pmid":"https://pubmed.ncbi.nlm.nih.gov/40343467"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf270","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf270","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf270/63136788/btaf270.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/btaf270/63136788/btaf270.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081314708","display_name":"Sagara N.S. Gurusinghe","orcid":null},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]},{"id":"https://openalex.org/I4210118921","display_name":"Institute of Life Sciences","ror":"https://ror.org/02927dx12","country_code":"IN","type":"education","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210118921","https://openalex.org/I4210134808"]}],"countries":["IL","IN"],"is_corresponding":true,"raw_author_name":"Sagara N S Gurusinghe","raw_affiliation_strings":["Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem , Jerusalem 9190401,","The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Department of Biological Chemistry, , Jerusalem,"],"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem , Jerusalem 9190401,","institution_ids":["https://openalex.org/I197251160"]},{"raw_affiliation_string":"The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Department of Biological Chemistry, , Jerusalem,","institution_ids":["https://openalex.org/I197251160","https://openalex.org/I4210118921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023874783","display_name":"Yibing Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yibing Wu","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco , CA 94158,","School of Pharmacy, University of California San Francisco Department of Pharmaceutical Chemistry, , CA"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco , CA 94158,","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"School of Pharmacy, University of California San Francisco Department of Pharmaceutical Chemistry, , CA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021623971","display_name":"William F. DeGrado","orcid":"https://orcid.org/0000-0003-4745-263X"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William DeGrado","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco , CA 94158,","School of Pharmacy, University of California San Francisco Department of Pharmaceutical Chemistry, , CA"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco , CA 94158,","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"School of Pharmacy, University of California San Francisco Department of Pharmaceutical Chemistry, , CA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004000734","display_name":"Julia M. Shifman","orcid":"https://orcid.org/0000-0001-6678-6497"},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]},{"id":"https://openalex.org/I4210118921","display_name":"Institute of Life Sciences","ror":"https://ror.org/02927dx12","country_code":"IN","type":"education","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210118921","https://openalex.org/I4210134808"]}],"countries":["IL","IN"],"is_corresponding":false,"raw_author_name":"Julia M Shifman","raw_affiliation_strings":["Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem , Jerusalem 9190401,","The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Department of Biological Chemistry, , Jerusalem,"],"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem , Jerusalem 9190401,","institution_ids":["https://openalex.org/I197251160"]},{"raw_affiliation_string":"The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Department of Biological Chemistry, , Jerusalem,","institution_ids":["https://openalex.org/I197251160","https://openalex.org/I4210118921"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5081314708"],"corresponding_institution_ids":["https://openalex.org/I197251160","https://openalex.org/I4210118921"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.0502,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.9100641,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"41","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9905999898910522,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9905999898910522,"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":0.9828000068664551,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9825000166893005,"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":0.6366710662841797},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6139325499534607},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.601233720779419},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.4775291681289673},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4753113389015198},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4571838080883026},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.4350336194038391},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40140387415885925},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1960790455341339},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18214234709739685},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1112649142742157}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6366710662841797},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6139325499534607},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.601233720779419},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.4775291681289673},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4753113389015198},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4571838080883026},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.4350336194038391},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40140387415885925},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1960790455341339},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18214234709739685},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1112649142742157}],"mesh":[{"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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/btaf270","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf270","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf270/63136788/btaf270.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:40343467","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40343467","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:europepmc.org:10963808","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12151015","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf270","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf270","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf270/63136788/btaf270.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":[],"awards":[{"id":"https://openalex.org/G5029724455","display_name":null,"funder_award_id":"3486/20","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306740","display_name":"Israel Cancer Research Fund","ror":"https://ror.org/02h43gk75"},{"id":"https://openalex.org/F4320321950","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017"},{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410233685.pdf","grobid_xml":"https://content.openalex.org/works/W4410233685.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W769759530","https://openalex.org/W1570416110","https://openalex.org/W1963697504","https://openalex.org/W1978287590","https://openalex.org/W1989181256","https://openalex.org/W1992006348","https://openalex.org/W1998222399","https://openalex.org/W1999390565","https://openalex.org/W2012427806","https://openalex.org/W2023350260","https://openalex.org/W2028286374","https://openalex.org/W2037048830","https://openalex.org/W2061922642","https://openalex.org/W2068190879","https://openalex.org/W2070506154","https://openalex.org/W2078302553","https://openalex.org/W2092387745","https://openalex.org/W2103459989","https://openalex.org/W2103860090","https://openalex.org/W2117541321","https://openalex.org/W2126523446","https://openalex.org/W2138865250","https://openalex.org/W2155030096","https://openalex.org/W2307896283","https://openalex.org/W2332100295","https://openalex.org/W2340330302","https://openalex.org/W2345331290","https://openalex.org/W2554576124","https://openalex.org/W2741292700","https://openalex.org/W2953103783","https://openalex.org/W2999242142","https://openalex.org/W3007500173","https://openalex.org/W3015602557","https://openalex.org/W3015878092","https://openalex.org/W3048714202","https://openalex.org/W3082121129","https://openalex.org/W3088578860","https://openalex.org/W3120180752","https://openalex.org/W3177500196","https://openalex.org/W3197477793","https://openalex.org/W3204640131","https://openalex.org/W4220685469","https://openalex.org/W4296032638","https://openalex.org/W4307568284","https://openalex.org/W4391308485"],"related_works":["https://openalex.org/W2155835698","https://openalex.org/W2076096978","https://openalex.org/W2094337488","https://openalex.org/W2350587855","https://openalex.org/W2044028228","https://openalex.org/W2994288809","https://openalex.org/W2077224613","https://openalex.org/W2047730886","https://openalex.org/W4240785775","https://openalex.org/W2027223071"],"abstract_inverted_index":{"ProBASS":[0],"is":[1],"available":[2],"at:":[3],"https://colab.research.google.com/github/sagagugit/ProBASS/blob/main/ProBASS.ipynb.":[4]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
