{"id":"https://openalex.org/W4416177928","doi":"https://doi.org/10.1371/journal.pcbi.1013679","title":"OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders","display_name":"OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders","publication_year":2025,"publication_date":"2025-11-13","ids":{"openalex":"https://openalex.org/W4416177928","doi":"https://doi.org/10.1371/journal.pcbi.1013679","pmid":"https://pubmed.ncbi.nlm.nih.gov/41231876"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013679","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013679","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1013679","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114637772","display_name":"Klemens Fl\u00f6ge","orcid":null},"institutions":[{"id":"https://openalex.org/I4210134004","display_name":"The Priory Hospital","ror":"https://ror.org/034w9e597","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210104184","https://openalex.org/I4210134004"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Klemens Fl\u00f6ge","raw_affiliation_strings":["Helmholtz AI, Munich, Germany","PriorLabs, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Helmholtz AI, Munich, Germany","institution_ids":[]},{"raw_affiliation_string":"PriorLabs, Berlin, Germany","institution_ids":["https://openalex.org/I4210134004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114658057","display_name":"Srisruthi Udayakumar","orcid":null},"institutions":[{"id":"https://openalex.org/I4210128379","display_name":"Orthopaedic Research Group","ror":"https://ror.org/02pfaex92","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210128379"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Srisruthi Udayakumar","raw_affiliation_strings":["Independent Researcher, Coimbatore, Tamil Nadu, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Independent Researcher, Coimbatore, Tamil Nadu, India","institution_ids":["https://openalex.org/I4210128379"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114658058","display_name":"Johanna Sommer","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Johanna Sommer","raw_affiliation_strings":["Munich Data Science Institute, Technical University of Munich, Garching, Germany","School of Computation, Information and Technology, Technical University of Munich, Garching, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Munich Data Science Institute, Technical University of Munich, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"School of Computation, Information and Technology, Technical University of Munich, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005966038","display_name":"Marie Piraud","orcid":"https://orcid.org/0000-0002-4917-2458"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Marie Piraud","raw_affiliation_strings":["Helmholtz Munich, Neuherberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Helmholtz Munich, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053642050","display_name":"Stefan Kesselheim","orcid":"https://orcid.org/0000-0003-0940-5752"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Stefan Kesselheim","raw_affiliation_strings":["Helmholtz AI, Munich, Germany","J\u00fclich Supercomputing Centre, Forschungszentrum J\u00fclich, J\u00fclich, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Helmholtz AI, Munich, Germany","institution_ids":[]},{"raw_affiliation_string":"J\u00fclich Supercomputing Centre, Forschungszentrum J\u00fclich, J\u00fclich, Germany","institution_ids":["https://openalex.org/I171892758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010706885","display_name":"Vincent Fortuin","orcid":"https://orcid.org/0000-0002-0640-2671"},"institutions":[{"id":"https://openalex.org/I4403386549","display_name":"Munich Center for Machine Learning","ror":"https://ror.org/02nfy3535","country_code":null,"type":"education","lineage":["https://openalex.org/I4403386549","https://openalex.org/I62916508","https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Vincent Fortuin","raw_affiliation_strings":["Helmholtz AI, Munich, Germany","Munich Center for Machine Learning, Munich, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Helmholtz AI, Munich, Germany","institution_ids":[]},{"raw_affiliation_string":"Munich Center for Machine Learning, Munich, Germany","institution_ids":["https://openalex.org/I4403386549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074504351","display_name":"Stephan G\u00fcnnemann","orcid":null},"institutions":[{"id":"https://openalex.org/I4403386549","display_name":"Munich Center for Machine Learning","ror":"https://ror.org/02nfy3535","country_code":null,"type":"education","lineage":["https://openalex.org/I4403386549","https://openalex.org/I62916508","https://openalex.org/I8204097"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Stephan G\u00fcnnemann","raw_affiliation_strings":["Munich Center for Machine Learning, Munich, Germany","Munich Data Science Institute, Technical University of Munich, Garching, Germany","School of Computation, Information and Technology, Technical University of Munich, Garching, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Munich Center for Machine Learning, Munich, Germany","institution_ids":["https://openalex.org/I4403386549"]},{"raw_affiliation_string":"Munich Data Science Institute, Technical University of Munich, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"School of Computation, Information and Technology, Technical University of Munich, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032889918","display_name":"Karel van der Weg","orcid":"https://orcid.org/0000-0002-1896-0291"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Karel J. van der Weg","raw_affiliation_strings":["Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany","Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich, J\u00fclich, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich, J\u00fclich, Germany","institution_ids":["https://openalex.org/I171892758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063949219","display_name":"Holger Gohlke","orcid":"https://orcid.org/0000-0001-8613-1447"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Holger Gohlke","raw_affiliation_strings":["Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany","Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich, J\u00fclich, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8613-1447","affiliations":[{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich, J\u00fclich, Germany","institution_ids":["https://openalex.org/I171892758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044354384","display_name":"Erin\u00e7 Merdivan","orcid":"https://orcid.org/0009-0004-9213-7393"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Erinc Merdivan","raw_affiliation_strings":["Helmholtz Munich, Neuherberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Helmholtz Munich, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023066254","display_name":"Alina Bazarova","orcid":"https://orcid.org/0000-0001-8874-1783"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Alina Bazarova","raw_affiliation_strings":["Helmholtz AI, Munich, Germany","J\u00fclich Supercomputing Centre, Forschungszentrum J\u00fclich, J\u00fclich, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8874-1783","affiliations":[{"raw_affiliation_string":"Helmholtz AI, Munich, Germany","institution_ids":[]},{"raw_affiliation_string":"J\u00fclich Supercomputing Centre, Forschungszentrum J\u00fclich, J\u00fclich, Germany","institution_ids":["https://openalex.org/I171892758"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5005966038","https://openalex.org/A5010706885","https://openalex.org/A5023066254","https://openalex.org/A5032889918","https://openalex.org/A5044354384","https://openalex.org/A5053642050","https://openalex.org/A5063949219","https://openalex.org/A5074504351","https://openalex.org/A5114637772","https://openalex.org/A5114658057","https://openalex.org/A5114658058"],"corresponding_institution_ids":["https://openalex.org/I171892758","https://openalex.org/I3018134672","https://openalex.org/I4210128379","https://openalex.org/I4210134004","https://openalex.org/I4403386549","https://openalex.org/I44260953","https://openalex.org/I62916508"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.8764,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.87018609,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"21","issue":"11","first_page":"e1013679","last_page":"e1013679"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.3255999982357025,"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":0.3255999982357025,"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":0.17589999735355377,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.07680000364780426,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.45649999380111694},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.436599999666214},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.43290001153945923},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4300000071525574},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4287000000476837},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.41449999809265137},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.4059999883174896},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.39879998564720154},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.39430001378059387}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6557999849319458},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6151000261306763},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.45649999380111694},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.44119998812675476},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.436599999666214},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.43290001153945923},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4300000071525574},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4287000000476837},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.41449999809265137},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.4059999883174896},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.39879998564720154},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.39430001378059387},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3840999901294708},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.3783999979496002},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.3619000017642975},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.35530000925064087},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.35199999809265137},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35010001063346863},{"id":"https://openalex.org/C2780226545","wikidata":"https://www.wikidata.org/wiki/Q6888030","display_name":"Modality (human\u2013computer interaction)","level":2,"score":0.32670000195503235},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2946999967098236},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.29019999504089355},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.2879999876022339},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.28790000081062317},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.26919999718666077},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.267300009727478},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.25609999895095825}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013679","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013679","pdf_url":null,"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:41231876","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41231876","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:doaj.org/article:a0f98a2aae394cf590c68e524ba96ed2","is_oa":true,"landing_page_url":"https://doaj.org/article/a0f98a2aae394cf590c68e524ba96ed2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 11, p e1013679 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11422781","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12614600","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:10.1371/journal.pcbi.1013679","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013679","pdf_url":null,"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":[],"awards":[{"id":"https://openalex.org/G598855922","display_name":null,"funder_award_id":"VSK33, FOUND","funder_id":"https://openalex.org/F4320331625","funder_display_name":"Gauss Centre for Supercomputing"}],"funders":[{"id":"https://openalex.org/F4320320923","display_name":"Branco Weiss Fellowship \u2013 Society in Science","ror":"https://ror.org/05a28rw58"},{"id":"https://openalex.org/F4320331625","display_name":"Gauss Centre for Supercomputing","ror":"https://ror.org/0585fsj26"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W2134672568","https://openalex.org/W2168310604","https://openalex.org/W2730472814","https://openalex.org/W2887981960","https://openalex.org/W2900167333","https://openalex.org/W2943495267","https://openalex.org/W2950954328","https://openalex.org/W2968494487","https://openalex.org/W3014805132","https://openalex.org/W3015921770","https://openalex.org/W3046375318","https://openalex.org/W3095259979","https://openalex.org/W3133458480","https://openalex.org/W3164046276","https://openalex.org/W3198227882","https://openalex.org/W3211795435","https://openalex.org/W3211951295","https://openalex.org/W4223581484","https://openalex.org/W4286500588","https://openalex.org/W4307068738","https://openalex.org/W4309908854","https://openalex.org/W4312197262","https://openalex.org/W4317717793","https://openalex.org/W4318071656","https://openalex.org/W4323438785","https://openalex.org/W4362471278","https://openalex.org/W4386071707","https://openalex.org/W4391431979","https://openalex.org/W4391849830","https://openalex.org/W4391873096","https://openalex.org/W4396895148","https://openalex.org/W4400231442","https://openalex.org/W4401391156","https://openalex.org/W4401730694","https://openalex.org/W4404942814","https://openalex.org/W4406234938","https://openalex.org/W4408062411","https://openalex.org/W4409451928","https://openalex.org/W4411799204"],"related_works":[],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,53,88,98,150,188,207],"Artificial":[3],"Intelligence":[4],"have":[5],"enabled":[6],"multi-modal":[7,25,96,198],"systems":[8,97],"to":[9,128,164,172],"model":[10,28],"and":[11,19,36,81,91,113,138,141,213],"translate":[12],"diverse":[13],"information":[14,124],"spaces.":[15],"Extending":[16],"beyond":[17],"text":[18],"vision,":[20],"we":[21,159],"introduce":[22],"OneProt,":[23],"a":[24,54,75,103],"Deep":[26],"Learning":[27,101],"for":[29,134,204],"proteins":[30,148],"that":[31,58,168],"integrates":[32],"structural,":[33],"sequence,":[34],"text,":[35],"binding":[37,114,180],"site":[38,115,181],"data.":[39],"Using":[40],"the":[41,46,93,120,129,154,166,170,176,179,195,202],"ImageBind":[42],"framework,":[43],"OneProt":[44,118],"aligns":[45],"latent":[47,155],"spaces":[48],"of":[49,77,95,106,122,178,197],"protein":[50,199,214],"modality":[51,162],"encoders":[52,127,167],"lightweight":[55],"fine-tuning":[56],"scheme":[57],"focuses":[59],"on":[60],"pairwise":[61],"alignment":[62],"with":[63],"sequence":[64,130],"data,":[65],"rather":[66],"than":[67],"requiring":[68],"full":[69],"matches.":[70],"This":[71,192],"novel":[72],"approach":[73],"comprises":[74],"mix":[76],"Graph":[78],"Neural":[79],"Networks":[80],"transformer":[82],"architectures.":[83],"It":[84],"demonstrates":[85],"good":[86],"performance":[87],"retrieval":[89],"tasks":[90],"showcases":[92],"efficacy":[94],"Protein":[99],"Machine":[100],"through":[102],"broad":[104],"spectrum":[105],"downstream":[107],"baselines,":[108],"including":[109],"enzyme":[110],"function":[111],"prediction":[112],"analysis.":[116],"Furthermore,":[117],"enables":[119],"transfer":[121],"representational":[123,143],"from":[125],"specialized":[126],"encoder,":[131,182],"enhancing":[132],"capabilities":[133],"distinguishing":[135],"evolutionarily":[136,146],"related":[137,147],"unrelated":[139],"sequences":[140],"exhibiting":[142],"properties":[144],"where":[145],"align":[149],"similar":[151,189],"directions":[152],"within":[153],"space.":[156],"In":[157],"addition,":[158],"extensively":[160],"investigate":[161],"ablations":[163],"identify":[165],"contribute":[169],"most":[171],"predictive":[173],"performance,":[174],"highlighting":[175],"significance":[177],"which":[183],"has":[184],"not":[185],"been":[186],"used":[187],"models":[190],"previously.":[191],"work":[193],"expands":[194],"horizons":[196],"models,":[200],"paving":[201],"way":[203],"transformative":[205],"applications":[206],"drug":[208],"discovery,":[209],"biocatalytic":[210],"reaction":[211],"planning,":[212],"engineering.":[215]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-11-13T00:00:00"}