{"id":"https://openalex.org/W4391115887","doi":"https://doi.org/10.1186/s12859-024-05637-5","title":"Tpgen: a language model for stable protein design with a specific topology structure","display_name":"Tpgen: a language model for stable protein design with a specific topology structure","publication_year":2024,"publication_date":"2024-01-23","ids":{"openalex":"https://openalex.org/W4391115887","doi":"https://doi.org/10.1186/s12859-024-05637-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/38254030"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05637-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05637-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05637-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05637-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090466533","display_name":"Xiaoping Min","orcid":"https://orcid.org/0000-0002-0817-0878"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoping Min","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Informatics, Institute of Artificial Intelligence, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Informatics, Institute of Artificial Intelligence, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110583552","display_name":"Chongzhou Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chongzhou Yang","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Informatics, Institute of Artificial Intelligence, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Informatics, Institute of Artificial Intelligence, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016278248","display_name":"Jun Xie","orcid":"https://orcid.org/0000-0002-1444-9234"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Xie","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Informatics, Institute of Artificial Intelligence, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Informatics, Institute of Artificial Intelligence, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047327093","display_name":"Yang Huang","orcid":"https://orcid.org/0000-0002-6458-6069"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Huang","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Life Sciences, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Life Sciences, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100367554","display_name":"Nan Liu","orcid":"https://orcid.org/0000-0003-3610-4883"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Nan Liu","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102603324","display_name":"Xiaocheng Jin","orcid":null},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaocheng Jin","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100690939","display_name":"Tianshu Wang","orcid":"https://orcid.org/0000-0001-7368-6881"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianshu Wang","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Informatics, Institute of Artificial Intelligence, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Informatics, Institute of Artificial Intelligence, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038086854","display_name":"Zhibo Kong","orcid":null},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhibo Kong","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045955292","display_name":"Xiaoli Lu","orcid":"https://orcid.org/0000-0003-1717-2610"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoli Lu","raw_affiliation_strings":["Information and Networking Center, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Networking Center, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009905256","display_name":"Shengxiang Ge","orcid":"https://orcid.org/0000-0002-7165-3004"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shengxiang Ge","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China. sxge@xmu.edu.cn","School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China. sxge@xmu.edu.cn","State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China. sxge@xmu.edu.cn","National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China. sxge@xmu.edu.cn","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China. sxge@xmu.edu.cn","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China. sxge@xmu.edu.cn","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100433188","display_name":"Jun Zhang","orcid":"https://orcid.org/0000-0002-6601-9180"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Zhang","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078732636","display_name":"Ningshao Xia","orcid":"https://orcid.org/0000-0003-0179-5266"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ningshao Xia","raw_affiliation_strings":["National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Centers of Biologic Products, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"School of Public Health, Xiamen University, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, No. 422 Siming South Rd, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5009905256"],"corresponding_institution_ids":["https://openalex.org/I191208505"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5598,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.63148373,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"25","issue":"1","first_page":"35","last_page":"35"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5741000175476074,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5741000175476074,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.14730000495910645,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.05400000140070915,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.592274010181427},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5375916957855225},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.5256301760673523},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5081527233123779},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33912768959999084},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.32581526041030884},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29533886909484863},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19238609075546265},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18224352598190308},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13334643840789795}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.592274010181427},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5375916957855225},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5256301760673523},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5081527233123779},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33912768959999084},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.32581526041030884},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29533886909484863},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19238609075546265},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18224352598190308},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13334643840789795},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05637-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05637-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05637-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38254030","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38254030","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10804651","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10804651","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10804651/pdf/12859_2024_Article_5637.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:1016db6fe276401eae6765f8e74a89ee","is_oa":true,"landing_page_url":"https://doaj.org/article/1016db6fe276401eae6765f8e74a89ee","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":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-18 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05637-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05637-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05637-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1409521295","display_name":null,"funder_award_id":"20720220005","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G5570595420","display_name":null,"funder_award_id":"62272399","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6672664789","display_name":null,"funder_award_id":"20720220006","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G7352761591","display_name":null,"funder_award_id":"20720220005 and 20720220006","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8526206718","display_name":null,"funder_award_id":"2019RU022","funder_id":"https://openalex.org/F4320323137","funder_display_name":"Chinese Academy of Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320323137","display_name":"Chinese Academy of Medical Sciences","ror":"https://ror.org/03cve4549"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391115887.pdf"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1981276685","https://openalex.org/W1991794210","https://openalex.org/W2004461664","https://openalex.org/W2020828286","https://openalex.org/W2024225780","https://openalex.org/W2035687084","https://openalex.org/W2055043387","https://openalex.org/W2106140689","https://openalex.org/W2124371326","https://openalex.org/W2150981663","https://openalex.org/W2165150801","https://openalex.org/W2520613901","https://openalex.org/W2538176089","https://openalex.org/W2735621019","https://openalex.org/W2759860792","https://openalex.org/W2773987374","https://openalex.org/W2785273668","https://openalex.org/W2913866568","https://openalex.org/W2963026768","https://openalex.org/W2964268978","https://openalex.org/W3027325047","https://openalex.org/W3037888463","https://openalex.org/W3042130878","https://openalex.org/W3084236163","https://openalex.org/W3100751385","https://openalex.org/W3105389349","https://openalex.org/W3114990254","https://openalex.org/W3127426316","https://openalex.org/W3135130381","https://openalex.org/W3135156311","https://openalex.org/W3135175179","https://openalex.org/W3137047737","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3194855384","https://openalex.org/W3197995571","https://openalex.org/W3204784544","https://openalex.org/W3216341763","https://openalex.org/W4200079908","https://openalex.org/W4210861939","https://openalex.org/W4210922059","https://openalex.org/W4220888452","https://openalex.org/W4225080234","https://openalex.org/W4282915889","https://openalex.org/W4283390570","https://openalex.org/W4283588088","https://openalex.org/W4288066876","https://openalex.org/W4296032638","https://openalex.org/W4309699634","https://openalex.org/W4312198087","https://openalex.org/W4318071656","https://openalex.org/W4376108605","https://openalex.org/W6630827713","https://openalex.org/W6761133114"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2118505788","https://openalex.org/W4254166511","https://openalex.org/W2150084125","https://openalex.org/W1542823905","https://openalex.org/W1490878237","https://openalex.org/W2990314835","https://openalex.org/W2131319730","https://openalex.org/W2059850119"],"abstract_inverted_index":{"BACKGROUND:":[0],"Natural":[1],"proteins":[2,14,41],"occupy":[3],"a":[4,17,62,69,80,102,108,159],"small":[5,40,124],"portion":[6],"of":[7,20,61,79,82,89,121,165],"the":[8,23,59,134,143,147],"protein":[9,125,138],"sequence":[10,24],"space,":[11],"whereas":[12],"artificial":[13],"can":[15,156],"explore":[16],"wider":[18],"range":[19],"possibilities":[21],"within":[22],"space.":[25],"However,":[26],"specific":[27],"requirements":[28],"may":[29],"not":[30],"be":[31],"met":[32],"when":[33],"generating":[34],"sequences":[35,77,126,139],"blindly.":[36],"Research":[37],"indicates":[38],"that":[39,117,140],"have":[42],"notable":[43],"advantages,":[44],"including":[45],"high":[46],"stability,":[47],"accurate":[48],"resolution":[49],"prediction,":[50],"and":[51,94,146,149],"facile":[52],"specificity":[53],"modification.":[54],"RESULTS:":[55],"This":[56],"study":[57,155],"involves":[58],"construction":[60],"neural":[63],"network":[64],"model":[65,73,105],"named":[66],"TopoProGenerator(TPGen)":[67],"using":[68],"transformer":[70],"decoder.":[71],"The":[72,86,114],"is":[74,119],"trained":[75,106],"with":[76,107,127],"consisting":[78],"maximum":[81],"65":[83],"amino":[84],"acids.":[85],"training":[87],"process":[88],"TopoProGenerator":[90,118],"incorporates":[91],"reinforcement":[92],"learning":[93],"adversarial":[95],"learning,":[96],"for":[97,161],"fine-tuning.":[98],"Additionally,":[99],"it":[100],"encompasses":[101],"stability":[103],"predictive":[104],"dataset":[109],"comprising":[110],"over":[111],"200,000":[112],"sequences.":[113],"results":[115],"demonstrate":[116],"capable":[120],"designing":[122,162],"stable":[123],"specified":[128,144],"topology":[129],"structures.":[130],"CONCLUSION:":[131],"TPGen":[132],"has":[133],"ability":[135],"to":[136],"generate":[137],"fold":[141],"into":[142],"topology,":[145],"pretraining":[148],"fine-tuning":[150],"methods":[151],"proposed":[152],"in":[153],"this":[154],"serve":[157],"as":[158],"framework":[160],"various":[163],"types":[164],"proteins.":[166]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}
