{"id":"https://openalex.org/W4411644384","doi":"https://doi.org/10.1021/acs.jcim.5c00585","title":"ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models","display_name":"ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models","publication_year":2025,"publication_date":"2025-06-25","ids":{"openalex":"https://openalex.org/W4411644384","doi":"https://doi.org/10.1021/acs.jcim.5c00585","pmid":"https://pubmed.ncbi.nlm.nih.gov/40560205"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00585","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00585","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","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"]},{"id":"https://openalex.org/I4210137189","display_name":"Center for Interdisciplinary Studies","ror":"https://ror.org/03whr7s66","country_code":"IN","type":"facility","lineage":["https://openalex.org/I4210137189"]}],"countries":["CN","IN"],"is_corresponding":false,"raw_author_name":"Zicheng Ma","raw_affiliation_strings":["Academy for Advanced Interdisciplinary Studies","Changping Laboratory","Peking University","Changping Laboratory, Beijing 102200, China"],"raw_orcid":"https://orcid.org/0000-0002-2844-1217","affiliations":[{"raw_affiliation_string":"Academy for Advanced Interdisciplinary Studies","institution_ids":["https://openalex.org/I4210137189"]},{"raw_affiliation_string":"Changping Laboratory","institution_ids":[]},{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Changping Laboratory, Beijing 102200, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055471144","display_name":"Chuanliu Fan","orcid":"https://orcid.org/0000-0001-9958-9537"},"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"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuanliu Fan","raw_affiliation_strings":["School of Computer Science and Technology","Soochow University","School of Computer Science and Technology, Soochow University, Suzhou 215006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"Soochow University","institution_ids":[]},{"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":null,"display_name":"Zhicong Wang","orcid":"https://orcid.org/0009-0005-8011-3228"},"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"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhicong Wang","raw_affiliation_strings":["School of Computer Science and Technology","Soochow University","School of Computer Science and Technology, Soochow University, Suzhou 215006, China"],"raw_orcid":"https://orcid.org/0009-0005-8011-3228","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"Soochow University","institution_ids":[]},{"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/A5100422927","display_name":"Zhen\u2010Yu Chen","orcid":"https://orcid.org/0000-0001-5615-1682"},"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"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenyu Chen","raw_affiliation_strings":["Beijing National Laboratory for Molecular Sciences","New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering","Peking University","Beijing National Laboratory for Molecular Sciences, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing National Laboratory for Molecular Sciences","institution_ids":["https://openalex.org/I4210116048"]},{"raw_affiliation_string":"New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering","institution_ids":[]},{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Beijing National Laboratory for Molecular Sciences, Beijing 100871, China","institution_ids":["https://openalex.org/I4210116048"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104118938","display_name":"Xiaohan Lin","orcid":"https://orcid.org/0009-0000-3705-5038"},"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"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohan Lin","raw_affiliation_strings":["Beijing National Laboratory for Molecular Sciences","New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering","Peking University","Beijing National Laboratory for Molecular Sciences, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing National Laboratory for Molecular Sciences","institution_ids":["https://openalex.org/I4210116048"]},{"raw_affiliation_string":"New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering","institution_ids":[]},{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Beijing National Laboratory for Molecular Sciences, Beijing 100871, China","institution_ids":["https://openalex.org/I4210116048"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102863621","display_name":"Yanheng Li","orcid":"https://orcid.org/0000-0002-9767-3468"},"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"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanheng Li","raw_affiliation_strings":["Beijing National Laboratory for Molecular Sciences","New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering","Peking University","Beijing National Laboratory for Molecular Sciences, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing National Laboratory for Molecular Sciences","institution_ids":["https://openalex.org/I4210116048"]},{"raw_affiliation_string":"New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering","institution_ids":[]},{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Beijing National Laboratory for Molecular Sciences, Beijing 100871, China","institution_ids":["https://openalex.org/I4210116048"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083733443","display_name":"Shihao Feng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shihao Feng","raw_affiliation_strings":["Changping Laboratory","Changping Laboratory, Beijing 102200, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Changping Laboratory","institution_ids":[]},{"raw_affiliation_string":"Changping Laboratory, Beijing 102200, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102007730","display_name":"Ziqiang Cao","orcid":"https://orcid.org/0000-0002-1077-9033"},"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"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ziqiang Cao","raw_affiliation_strings":["School of Computer Science and Technology","Soochow University","School of Computer Science and Technology, Soochow University, Suzhou 215006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"Soochow University","institution_ids":[]},{"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/A5100433211","display_name":"Jun Zhang","orcid":"https://orcid.org/0000-0002-8760-6747"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Jun Zhang","raw_affiliation_strings":["Changping Laboratory","Changping Laboratory, Beijing 102200, China"],"raw_orcid":"https://orcid.org/0000-0002-8760-6747","affiliations":[{"raw_affiliation_string":"Changping Laboratory","institution_ids":[]},{"raw_affiliation_string":"Changping Laboratory, Beijing 102200, 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"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yi Qin Gao","raw_affiliation_strings":["Beijing National Laboratory for Molecular Sciences","Changping Laboratory","New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering","Peking University","Changping Laboratory, Beijing 102200, China","Beijing National Laboratory for Molecular Sciences, Beijing 100871, China"],"raw_orcid":"https://orcid.org/0000-0002-4309-9376","affiliations":[{"raw_affiliation_string":"Beijing National Laboratory for Molecular Sciences","institution_ids":["https://openalex.org/I4210116048"]},{"raw_affiliation_string":"Changping Laboratory","institution_ids":[]},{"raw_affiliation_string":"New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering","institution_ids":[]},{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Changping Laboratory, Beijing 102200, China","institution_ids":[]},{"raw_affiliation_string":"Beijing National Laboratory for Molecular Sciences, Beijing 100871, China","institution_ids":["https://openalex.org/I4210116048"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5051732177","https://openalex.org/A5100433211","https://openalex.org/A5102007730"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I3923682","https://openalex.org/I4210116048","https://openalex.org/I4390039265"],"apc_list":null,"apc_paid":null,"fwci":4.2681,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.94422592,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"65","issue":"13","first_page":"6599","last_page":"6612"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9907000064849854,"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":0.9907000064849854,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9836000204086304,"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":0.9825999736785889,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6239442825317383},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5971447825431824},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.46367478370666504},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.45524993538856506},{"id":"https://openalex.org/keywords/cognitive-science","display_name":"Cognitive science","score":0.41125285625457764},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3542026877403259},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.19647184014320374},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1339331865310669}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6239442825317383},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5971447825431824},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.46367478370666504},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.45524993538856506},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.41125285625457764},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3542026877403259},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.19647184014320374},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1339331865310669},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"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":"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c00585","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00585","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40560205","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40560205","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4243641284","display_name":null,"funder_award_id":"92353304","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5292414797","display_name":null,"funder_award_id":"T2495221","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"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/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":64,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1975147762","https://openalex.org/W2048822589","https://openalex.org/W2102245393","https://openalex.org/W2117486996","https://openalex.org/W2130479394","https://openalex.org/W2463955103","https://openalex.org/W2912083425","https://openalex.org/W2936695845","https://openalex.org/W2938704169","https://openalex.org/W2950595506","https://openalex.org/W2990138404","https://openalex.org/W3001279689","https://openalex.org/W3009321976","https://openalex.org/W3045928028","https://openalex.org/W3168867926","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3209056694","https://openalex.org/W4206759694","https://openalex.org/W4213149192","https://openalex.org/W4283026156","https://openalex.org/W4296032638","https://openalex.org/W4299527668","https://openalex.org/W4318071656","https://openalex.org/W4319165821","https://openalex.org/W4319653544","https://openalex.org/W4327550249","https://openalex.org/W4362515116","https://openalex.org/W4383957026","https://openalex.org/W4384112212","https://openalex.org/W4384918448","https://openalex.org/W4386080660","https://openalex.org/W4386469263","https://openalex.org/W4386556027","https://openalex.org/W4386708656","https://openalex.org/W4388213147","https://openalex.org/W4388627063","https://openalex.org/W4388694364","https://openalex.org/W4389068883","https://openalex.org/W4390872598","https://openalex.org/W4391047461","https://openalex.org/W4391912611","https://openalex.org/W4392222550","https://openalex.org/W4396721167","https://openalex.org/W4397049097","https://openalex.org/W4398243369","https://openalex.org/W4401306886","https://openalex.org/W4402671766","https://openalex.org/W4402671941","https://openalex.org/W4402672060","https://openalex.org/W4402705653","https://openalex.org/W4402727536","https://openalex.org/W4403799526","https://openalex.org/W4404377278","https://openalex.org/W4404458588","https://openalex.org/W4404781852","https://openalex.org/W4405095475","https://openalex.org/W4405627658","https://openalex.org/W4405766390","https://openalex.org/W4406261070","https://openalex.org/W4406440058","https://openalex.org/W4406779522","https://openalex.org/W4406810926"],"related_works":["https://openalex.org/W2169518243","https://openalex.org/W3188962172","https://openalex.org/W2772917594","https://openalex.org/W4312825515","https://openalex.org/W4306742369","https://openalex.org/W4303457083","https://openalex.org/W2131146434","https://openalex.org/W2951359407","https://openalex.org/W4376623224","https://openalex.org/W3204019825"],"abstract_inverted_index":{"Large":[0],"language":[1],"models":[2],"(LLMs)":[3],"have":[4],"made":[5],"remarkable":[6],"progress":[7],"in":[8,15,52,159,173],"the":[9,28,37,43,65,88,107,111,164,186,194,201],"field":[10],"of":[11,30,60,67,106,214],"molecular":[12,31],"science,":[13,36],"particularly":[14],"understanding":[16],"and":[17,73,92,119,127,142,181,197],"generating":[18],"functional":[19],"small":[20],"molecules.":[21],"This":[22,100],"success":[23],"is":[24],"largely":[25],"attributed":[26],"to":[27,125,208],"effectiveness":[29],"tokenization":[32],"strategies.":[33],"In":[34],"protein":[35,53,89,117,129,160,183],"amino":[38],"acid":[39],"sequence":[40],"serves":[41],"as":[42,138],"sole":[44],"tokenizer":[45],"for":[46,69],"LLMs.":[47],"However,":[48],"many":[49],"fundamental":[50],"challenges":[51],"science":[54],"are":[55],"inherently":[56],"structure-dependent.":[57],"The":[58],"absence":[59],"structure-aware":[61],"tokens":[62],"significantly":[63],"limits":[64],"capabilities":[66],"LLMs":[68,124,207],"comprehensive":[70],"biomolecular":[71],"comprehension":[72],"multimodal":[74,116],"generation.":[75,120],"To":[76],"address":[77,210],"these":[78],"challenges,":[79],"we":[80,189],"introduce":[81],"a":[82,96,170,211],"novel":[83],"framework,":[84],"ProtTeX,":[85],"which":[86],"tokenizes":[87],"sequences,":[90],"structures,":[91],"textual":[93],"information":[94,137],"into":[95],"unified":[97],"discrete":[98],"space.":[99],"innovative":[101],"approach":[102],"enables":[103,122,177],"joint":[104],"training":[105,196],"LLM":[108,202],"exclusively":[109],"through":[110,131],"Next-Token":[112],"Prediction":[113],"paradigm,":[114],"facilitating":[115],"reasoning":[118,140],"ProtTeX":[121,204],"general":[123],"perceive":[126],"process":[128],"structures":[130,146],"sequential":[132,148],"text":[133,149],"input,":[134],"leverage":[135],"structural":[136],"intermediate":[139],"components,":[141],"generate":[143],"or":[144],"manipulate":[145],"via":[147],"output.":[150],"Experiments":[151],"demonstrate":[152,190],"that":[153,191],"our":[154],"model":[155,168],"achieves":[156],"significant":[157],"improvements":[158],"function":[161],"prediction,":[162],"outperforming":[163],"state-of-the-art":[165],"domain":[166],"expert":[167],"with":[169],"2-fold":[171],"increase":[172],"accuracy.":[174],"Our":[175],"framework":[176],"high-quality":[178],"conformational":[179],"generation":[180],"customizable":[182],"design.":[184],"For":[185],"first":[187],"time,":[188],"by":[192],"adopting":[193],"standard":[195],"inference":[198],"pipelines":[199],"from":[200],"domain,":[203],"empowers":[205],"decoder-only":[206],"effectively":[209],"diverse":[212],"spectrum":[213],"protein-related":[215],"tasks.":[216]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
