{"id":"https://openalex.org/W4412701265","doi":"https://doi.org/10.1093/bioinformatics/btaf396","title":"Prot2Chat: protein large language model with early fusion of text, sequence, and structure","display_name":"Prot2Chat: protein large language model with early fusion of text, sequence, and structure","publication_year":2025,"publication_date":"2025-07-28","ids":{"openalex":"https://openalex.org/W4412701265","doi":"https://doi.org/10.1093/bioinformatics/btaf396","pmid":"https://pubmed.ncbi.nlm.nih.gov/40720216"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf396","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf396","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf396/63866323/btaf396.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/btaf396/63866323/btaf396.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005524411","display_name":"Zhicong Wang","orcid":"https://orcid.org/0000-0002-4238-9312"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhicong Wang","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University , Suzhou 215006,","School of Computer Science and Technology, Soochow University, Suzhou 215006, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University , Suzhou 215006,","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University, Suzhou 215006, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101191255","display_name":"Zicheng Ma","orcid":"https://orcid.org/0000-0002-2844-1217"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zicheng Ma","raw_affiliation_strings":["Changping Laboratory , Beijing 102206,","Changping Laboratory, Beijing 102206, China","Changping Laboratory, Peking University , Beijing, 102206,"],"affiliations":[{"raw_affiliation_string":"Changping Laboratory , Beijing 102206,","institution_ids":[]},{"raw_affiliation_string":"Changping Laboratory, Beijing 102206, China","institution_ids":[]},{"raw_affiliation_string":"Changping Laboratory, Peking University , Beijing, 102206,","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009421684","display_name":"Ziqiang Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziqiang Cao","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University , Suzhou 215006,","School of Computer Science and Technology, Soochow University, Suzhou 215006, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University , Suzhou 215006,","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University, Suzhou 215006, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101560057","display_name":"Changlong Zhou","orcid":"https://orcid.org/0000-0002-6387-4173"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Changlong Zhou","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University , Suzhou 215006,","School of Computer Science and Technology, Soochow University, Suzhou 215006, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University , Suzhou 215006,","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University, Suzhou 215006, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100433054","display_name":"Jun Zhang","orcid":"https://orcid.org/0000-0001-6990-5324"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Zhang","raw_affiliation_strings":["Changping Laboratory , Beijing 102206,","Changping Laboratory, Peking University , Beijing, 102206,","Changping Laboratory, Beijing 102206, China"],"affiliations":[{"raw_affiliation_string":"Changping Laboratory , Beijing 102206,","institution_ids":[]},{"raw_affiliation_string":"Changping Laboratory, Peking University , Beijing, 102206,","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Changping Laboratory, Beijing 102206, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051732177","display_name":"Yi Qin Gao","orcid":"https://orcid.org/0000-0002-4309-9376"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Qin Gao","raw_affiliation_strings":["Changping Laboratory , Beijing 102206,","Changping Laboratory, Beijing 102206, China","Changping Laboratory, Peking University , Beijing, 102206,"],"affiliations":[{"raw_affiliation_string":"Changping Laboratory , Beijing 102206,","institution_ids":[]},{"raw_affiliation_string":"Changping Laboratory, Beijing 102206, China","institution_ids":[]},{"raw_affiliation_string":"Changping Laboratory, Peking University , Beijing, 102206,","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5005524411"],"corresponding_institution_ids":["https://openalex.org/I3923682"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.4448,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.8941197,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"41","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9972000122070312,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9972000122070312,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9887999892234802,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9876000285148621,"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/sequence","display_name":"Sequence (biology)","score":0.6898902654647827},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5522253513336182},{"id":"https://openalex.org/keywords/fusion","display_name":"Fusion","score":0.5252113938331604},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48793384432792664},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3823970556259155},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3709715008735657},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22562983632087708},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16105258464813232},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.09565645456314087}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6898902654647827},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5522253513336182},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.5252113938331604},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48793384432792664},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3823970556259155},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3709715008735657},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22562983632087708},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16105258464813232},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.09565645456314087},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf396","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf396","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf396/63866323/btaf396.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:40720216","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40720216","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:12341678","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12341678","pdf_url":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf396","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf396","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf396/63866323/btaf396.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":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G543380124","display_name":null,"funder_award_id":"2022ZD0115002","funder_id":"https://openalex.org/F4320329860","funder_display_name":"National Science and Technology Major Project"}],"funders":[{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412701265.pdf","grobid_xml":"https://content.openalex.org/works/W4412701265.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1593271688","https://openalex.org/W2966590054","https://openalex.org/W3164046276","https://openalex.org/W4233120011","https://openalex.org/W4236358448","https://openalex.org/W4296032638","https://openalex.org/W4327550249","https://openalex.org/W4375858802","https://openalex.org/W4388627063","https://openalex.org/W4396721167","https://openalex.org/W4404377278","https://openalex.org/W4404708476","https://openalex.org/W4405745706","https://openalex.org/W4409525624"],"related_works":["https://openalex.org/W2099421762","https://openalex.org/W2530546662","https://openalex.org/W2967030268","https://openalex.org/W2185253430","https://openalex.org/W4210345652","https://openalex.org/W2112284452","https://openalex.org/W1984333081","https://openalex.org/W2945063165","https://openalex.org/W3188962172","https://openalex.org/W3204019825"],"abstract_inverted_index":{"The":[0],"models":[1],"and":[2],"codes":[3],"are":[4],"available":[5],"at":[6],"https://github.com/wangzc1233/Prot2Chat.":[7]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-07-28T00:00:00"}
