{"id":"https://openalex.org/W4399608215","doi":"https://doi.org/10.1093/bioinformatics/btae364","title":"HELM-GPT: <i>de novo</i> macrocyclic peptide design using generative pre-trained transformer","display_name":"HELM-GPT: <i>de novo</i> macrocyclic peptide design using generative pre-trained transformer","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4399608215","doi":"https://doi.org/10.1093/bioinformatics/btae364","pmid":"https://pubmed.ncbi.nlm.nih.gov/38867692"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae364","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae364","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae364/58212621/btae364.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/btae364/58212621/btae364.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014868273","display_name":"Xiaopeng Xu","orcid":"https://orcid.org/0000-0003-2414-7851"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Xiaopeng Xu","raw_affiliation_strings":["Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029195135","display_name":"Chencheng Xu","orcid":"https://orcid.org/0000-0002-2262-6966"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Chencheng Xu","raw_affiliation_strings":["Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042489447","display_name":"Wenjia He","orcid":"https://orcid.org/0000-0001-8161-4642"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Wenjia He","raw_affiliation_strings":["Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110758704","display_name":"Lesong Wei","orcid":null},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Lesong Wei","raw_affiliation_strings":["Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100369544","display_name":"Haoyang Li","orcid":"https://orcid.org/0000-0003-3164-8240"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Haoyang Li","raw_affiliation_strings":["Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071123136","display_name":"Juexiao Zhou","orcid":"https://orcid.org/0000-0002-6739-6236"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Juexiao Zhou","raw_affiliation_strings":["Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021422965","display_name":"Ruochi Zhang","orcid":"https://orcid.org/0000-0001-6541-4050"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ruochi Zhang","raw_affiliation_strings":["Syneron Technology , Guangzhou 510000, China"],"affiliations":[{"raw_affiliation_string":"Syneron Technology , Guangzhou 510000, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100445198","display_name":"Yu Wang","orcid":"https://orcid.org/0000-0002-3526-9494"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yu Wang","raw_affiliation_strings":["Syneron Technology , Guangzhou 510000, China"],"affiliations":[{"raw_affiliation_string":"Syneron Technology , Guangzhou 510000, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101973531","display_name":"Yuanpeng Xiong","orcid":"https://orcid.org/0000-0002-0393-6184"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yuanpeng Xiong","raw_affiliation_strings":["Syneron Technology , Guangzhou 510000, China"],"affiliations":[{"raw_affiliation_string":"Syneron Technology , Guangzhou 510000, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100618900","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0002-7108-3574"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Xin Gao","raw_affiliation_strings":["Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5014868273"],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.7416,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.90607313,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"40","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9983000159263611,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9983000159263611,"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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9929999709129333,"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/peptide","display_name":"Peptide","score":0.6002638339996338},{"id":"https://openalex.org/keywords/intracellular","display_name":"Intracellular","score":0.5916395783424377},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5147235989570618},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4698654115200043},{"id":"https://openalex.org/keywords/kras","display_name":"KRAS","score":0.4625403881072998},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.4491998553276062},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3510970175266266},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32297980785369873},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3012917637825012},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2902347445487976}],"concepts":[{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6002638339996338},{"id":"https://openalex.org/C79879829","wikidata":"https://www.wikidata.org/wiki/Q5571762","display_name":"Intracellular","level":2,"score":0.5916395783424377},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5147235989570618},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4698654115200043},{"id":"https://openalex.org/C2781187634","wikidata":"https://www.wikidata.org/wiki/Q20969980","display_name":"KRAS","level":4,"score":0.4625403881072998},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.4491998553276062},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3510970175266266},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32297980785369873},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3012917637825012},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2902347445487976},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae364","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae364","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae364/58212621/btae364.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:38867692","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38867692","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:11256930","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11256930","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae364","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae364","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae364/58212621/btae364.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/G2058729345","display_name":null,"funder_award_id":"FCC/1/1976-45-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5348541598","display_name":null,"funder_award_id":"URF/1/4352-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G8253667702","display_name":null,"funder_award_id":"FCC/1/1976-44-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399608215.pdf"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W2045093121","https://openalex.org/W2083224653","https://openalex.org/W2136359146","https://openalex.org/W2275655681","https://openalex.org/W2610148085","https://openalex.org/W2796306022","https://openalex.org/W2900090807","https://openalex.org/W2914542247","https://openalex.org/W3017609301","https://openalex.org/W3094686696","https://openalex.org/W3100839802","https://openalex.org/W3116865743","https://openalex.org/W3138308373","https://openalex.org/W3159343835","https://openalex.org/W3165171933","https://openalex.org/W4200031091","https://openalex.org/W4205953903","https://openalex.org/W4293461777","https://openalex.org/W4309269459","https://openalex.org/W4327694659","https://openalex.org/W4381848602","https://openalex.org/W4391972713"],"related_works":["https://openalex.org/W3030972949","https://openalex.org/W4283712951","https://openalex.org/W4229832877","https://openalex.org/W4306404900","https://openalex.org/W3111812619","https://openalex.org/W4248366929","https://openalex.org/W2590035663","https://openalex.org/W2914997899","https://openalex.org/W4229670017","https://openalex.org/W4226309907"],"abstract_inverted_index":{"The":[0],"code":[1],"and":[2],"data":[3],"of":[4],"HELM-GPT":[5],"are":[6],"freely":[7],"available":[8],"on":[9],"GitHub":[10],"(https://github.com/charlesxu90/helm-gpt).":[11]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
