{"id":"https://openalex.org/W4389137846","doi":"https://doi.org/10.1093/bib/bbad429","title":"Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling","display_name":"Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling","publication_year":2023,"publication_date":"2023-11-22","ids":{"openalex":"https://openalex.org/W4389137846","doi":"https://doi.org/10.1093/bib/bbad429","pmid":"https://pubmed.ncbi.nlm.nih.gov/38018910"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad429","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad429","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad429/55464751/bbad429.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad429/55464751/bbad429.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100370140","display_name":"Junjie Zhu","orcid":"https://orcid.org/0000-0001-7503-4502"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junjie Zhu","raw_affiliation_strings":["Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I183067930"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100623069","display_name":"Zhengxin Li","orcid":"https://orcid.org/0000-0002-9535-261X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhengxin Li","raw_affiliation_strings":["Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I183067930"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111110046","display_name":"Haowei Tong","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haowei Tong","raw_affiliation_strings":["Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I183067930"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101550257","display_name":"Zhouyu Lu","orcid":"https://orcid.org/0000-0002-8290-6038"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhouyu Lu","raw_affiliation_strings":["Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I183067930"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048727219","display_name":"Ning-Jie Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ningjie Zhang","raw_affiliation_strings":["Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I183067930"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057767596","display_name":"Ting Wei","orcid":"https://orcid.org/0000-0001-9008-0339"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ting Wei","raw_affiliation_strings":["Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I183067930"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100456783","display_name":"Haifeng Chen","orcid":"https://orcid.org/0000-0002-7496-4182"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hai-Feng Chen","raw_affiliation_strings":["Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I183067930"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism , Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, , Shanghai, 200240 , China","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5057767596","https://openalex.org/A5100456783"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210160507"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.1874,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.88017286,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"25","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9954000115394592,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6929949522018433},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5784797668457031},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.5453881025314331},{"id":"https://openalex.org/keywords/intrinsically-disordered-proteins","display_name":"Intrinsically disordered proteins","score":0.46360528469085693},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46248728036880493},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.445861279964447},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.44492414593696594},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3699166178703308},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3485962152481079},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.19156312942504883},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.16278553009033203},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.12274202704429626},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08235025405883789}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6929949522018433},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5784797668457031},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.5453881025314331},{"id":"https://openalex.org/C2778815515","wikidata":"https://www.wikidata.org/wiki/Q3408242","display_name":"Intrinsically disordered proteins","level":2,"score":0.46360528469085693},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46248728036880493},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.445861279964447},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.44492414593696594},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3699166178703308},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3485962152481079},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.19156312942504883},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.16278553009033203},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.12274202704429626},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08235025405883789},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","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":"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":"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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad429","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad429","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad429/55464751/bbad429.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38018910","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38018910","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10783862","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10783862","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10783862/pdf/bbad429.pdf","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad429","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad429","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad429/55464751/bbad429.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8299999833106995,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G1107294320","display_name":null,"funder_award_id":"2020YFA0907700","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1361707744","display_name":null,"funder_award_id":"2197706","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2376276132","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G2909483199","display_name":null,"funder_award_id":"YG2023LC03","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5497449960","display_name":null,"funder_award_id":"2020YFA0907700","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6665456538","display_name":null,"funder_award_id":"32171242","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6757240918","display_name":null,"funder_award_id":"2020YFA0907","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8654760","display_name":null,"funder_award_id":"21977068","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322999","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389137846.pdf"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W149235922","https://openalex.org/W1959608418","https://openalex.org/W2052126522","https://openalex.org/W2069123478","https://openalex.org/W2092002011","https://openalex.org/W2404280981","https://openalex.org/W2510867035","https://openalex.org/W2549686806","https://openalex.org/W2765861397","https://openalex.org/W2789997233","https://openalex.org/W2940537888","https://openalex.org/W2972246420","https://openalex.org/W2981350008","https://openalex.org/W2985353376","https://openalex.org/W2991470870","https://openalex.org/W3007324177","https://openalex.org/W3013264144","https://openalex.org/W3037337145","https://openalex.org/W3102548437","https://openalex.org/W3130801441","https://openalex.org/W3177828909","https://openalex.org/W3195375135","https://openalex.org/W3201385722","https://openalex.org/W3217536461","https://openalex.org/W4281478775","https://openalex.org/W4283164695","https://openalex.org/W4283588088","https://openalex.org/W4288027461","https://openalex.org/W4292060935","https://openalex.org/W4300980637","https://openalex.org/W4312198153","https://openalex.org/W4320040108","https://openalex.org/W4327550249","https://openalex.org/W4362679214","https://openalex.org/W4363674486","https://openalex.org/W4379919077","https://openalex.org/W4380352196","https://openalex.org/W4382283964","https://openalex.org/W4383872128","https://openalex.org/W4384030552","https://openalex.org/W4384407823","https://openalex.org/W6606005393","https://openalex.org/W6640963894","https://openalex.org/W6769849856","https://openalex.org/W6845397888","https://openalex.org/W6851317023","https://openalex.org/W6853063347","https://openalex.org/W6854092224"],"related_works":["https://openalex.org/W2914439699","https://openalex.org/W1966521458","https://openalex.org/W4225685368","https://openalex.org/W4225861603","https://openalex.org/W4200632766","https://openalex.org/W2925138603","https://openalex.org/W4309230501","https://openalex.org/W1966688840","https://openalex.org/W3045968455","https://openalex.org/W2006514416"],"abstract_inverted_index":{"The":[0,232],"biological":[1],"function":[2],"of":[3,19,42,125,230,256],"proteins":[4,171,222],"is":[5],"determined":[6],"not":[7,140],"only":[8],"by":[9,15,142],"their":[10,20,175],"static":[11,25],"structures":[12],"but":[13],"also":[14],"the":[16,116,227,243,254],"dynamic":[17,50],"properties":[18],"conformational":[21,77,149,262],"ensembles.":[22],"Numerous":[23],"high-accuracy":[24],"structure":[26],"prediction":[27],"tools":[28],"have":[29,57,91],"been":[30,92],"recently":[31],"developed":[32,93],"based":[33],"on":[34,59],"deep":[35,136,189],"learning;":[36],"however,":[37],"there":[38],"remains":[39],"a":[40,123,134,187,196,204,249,265],"lack":[41],"efficient":[43],"and":[44,72,109,120,128,146,203,219,240,264],"accurate":[45,214],"methods":[46],"for":[47,69,165,252],"exploring":[48],"protein":[49,55,201,215,261,267],"conformations.":[51],"Traditionally,":[52],"studies":[53],"concerning":[54],"dynamics":[56,61,107],"relied":[58],"molecular":[60,106],"(MD)":[62],"simulations,":[63],"which":[64,173],"incur":[65],"significant":[66],"computational":[67,126],"costs":[68],"all-atom":[70],"precision":[71],"struggle":[73],"to":[74,94,199,211,225],"adequately":[75],"sample":[76],"spaces":[78,150],"with":[79,208],"high":[80,238],"energy":[81,144],"barriers.":[82],"To":[83],"overcome":[84],"these":[85],"limitations,":[86],"various":[87],"enhanced":[88,100,179],"sampling":[89,96,101,112,180,210,228],"techniques":[90],"accelerate":[95],"in":[97,161,242],"MD.":[98],"Traditional":[99],"approaches":[102],"like":[103],"replica":[104],"exchange":[105],"(REMD)":[108],"frontier":[110],"expansion":[111],"(FEXS)":[113],"often":[114,158],"follow":[115],"MD":[117,257],"simulation":[118],"approach":[119],"still":[121],"cost":[122],"lot":[124],"resources":[127],"time.":[129],"Variational":[130],"autoencoders":[131],"(VAEs),":[132],"as":[133,177],"classic":[135],"generative":[137],"model,":[138],"are":[139],"restricted":[141],"potential":[143],"landscapes":[145],"can":[147],"explore":[148],"more":[151],"efficiently":[152],"than":[153],"traditional":[154],"methods.":[155],"However,":[156],"VAEs":[157],"face":[159],"challenges":[160],"generating":[162,259],"reasonable":[163],"conformations":[164],"complex":[166],"proteins,":[167],"especially":[168],"intrinsically":[169],"disordered":[170],"(IDPs),":[172],"limits":[174],"application":[176],"an":[178],"method.":[181],"In":[182],"this":[183],"study,":[184],"we":[185],"presented":[186],"novel":[188],"learning":[190],"model":[191],"(named":[192],"Phanto-IDP)":[193],"that":[194,235],"utilizes":[195],"graph-based":[197],"encoder":[198],"extract":[200],"features":[202],"transformer-based":[205],"decoder":[206],"combined":[207],"variational":[209],"generate":[212],"highly":[213],"backbones.":[216],"Ten":[217],"IDPs":[218],"four":[220],"structured":[221],"were":[223],"used":[224],"evaluate":[226],"ability":[229],"Phanto-IDP.":[231],"results":[233],"demonstrate":[234],"Phanto-IDP":[236],"has":[237],"fidelity":[239],"diversity":[241],"generated":[244],"conformation":[245],"ensembles,":[246],"making":[247],"it":[248],"suitable":[250],"tool":[251],"enhancing":[253],"efficiency":[255],"simulation,":[258],"broader":[260],"space":[263],"continuous":[266],"transition":[268],"path.":[269]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":9}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
