{"id":"https://openalex.org/W2927651842","doi":"https://doi.org/10.1186/s12859-019-2652-5","title":"Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling","display_name":"Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling","publication_year":2019,"publication_date":"2019-03-01","ids":{"openalex":"https://openalex.org/W2927651842","doi":"https://doi.org/10.1186/s12859-019-2652-5","mag":"2927651842","pmid":"https://pubmed.ncbi.nlm.nih.gov/30925867"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2652-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2652-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2652-5","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/s12859-019-2652-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100406986","display_name":"Chao Wang","orcid":"https://orcid.org/0000-0002-4316-8124"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chao Wang","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026288065","display_name":"Yi Wei","orcid":"https://orcid.org/0000-0002-3016-6816"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Wei","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060273621","display_name":"Haicang Zhang","orcid":"https://orcid.org/0000-0001-6268-4258"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haicang Zhang","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072891032","display_name":"Lupeng Kong","orcid":"https://orcid.org/0000-0002-0963-1293"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lupeng Kong","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108903761","display_name":"Shiwei Sun","orcid":"https://orcid.org/0000-0002-0351-3720"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiwei Sun","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021041719","display_name":"Wei\u2010Mou Zheng","orcid":"https://orcid.org/0000-0001-6546-2917"},"institutions":[{"id":"https://openalex.org/I4210125404","display_name":"Institute of Theoretical Physics","ror":"https://ror.org/02xtbq882","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210125404"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wei-Mou Zheng","raw_affiliation_strings":["Institute of Theoretical Physics, Chinese Academy of Sciences, 55, Zhongguancun East Road, Beijing, 100190, China. zheng@itp.ac.cn","University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China. zheng@itp.ac.cn","University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Theoretical Physics, Chinese Academy of Sciences, 55, Zhongguancun East Road, Beijing, 100190, China. zheng@itp.ac.cn","institution_ids":["https://openalex.org/I4210125404"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China. zheng@itp.ac.cn","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076729236","display_name":"Dongbo Bu","orcid":"https://orcid.org/0000-0003-4119-4238"},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dongbo Bu","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China. dbu@ict.ac.cn","University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China. dbu@ict.ac.cn","University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China. dbu@ict.ac.cn","institution_ids":["https://openalex.org/I4210090176"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China. dbu@ict.ac.cn","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 19-1, Yuquan Road, Shijingshan, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5021041719","https://openalex.org/A5076729236"],"corresponding_institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I4210125404","https://openalex.org/I4210165038"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.02210706,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"20","issue":"S3","first_page":"135","last_page":"135"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.954200029373169,"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":0.954200029373169,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.014800000004470348,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.010900000110268593,"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/attraction","display_name":"Attraction","score":0.8557038903236389},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.791832685470581},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"Energy landscape","score":0.6374020576477051},{"id":"https://openalex.org/keywords/structural-basin","display_name":"Structural basin","score":0.5791930556297302},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.5294382572174072},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4584782123565674},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4515782594680786},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.40578997135162354},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2920519709587097},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2247246503829956},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17633557319641113},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.1402018964290619},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.12893590331077576},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.07657834887504578}],"concepts":[{"id":"https://openalex.org/C2778364177","wikidata":"https://www.wikidata.org/wiki/Q2247133","display_name":"Attraction","level":2,"score":0.8557038903236389},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.791832685470581},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.6374020576477051},{"id":"https://openalex.org/C109007969","wikidata":"https://www.wikidata.org/wiki/Q749565","display_name":"Structural basin","level":2,"score":0.5791930556297302},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.5294382572174072},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4584782123565674},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4515782594680786},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.40578997135162354},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2920519709587097},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2247246503829956},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17633557319641113},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1402018964290619},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.12893590331077576},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.07657834887504578},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-2652-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2652-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2652-5","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:30925867","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30925867","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:doaj.org/article:6ed28e082ad847f19e2703f86cd71abd","is_oa":true,"landing_page_url":"https://doaj.org/article/6ed28e082ad847f19e2703f86cd71abd","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 20, Iss S3, Pp 99-108 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5441294","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6439974","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2652-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2652-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2652-5","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":[{"score":0.9100000262260437,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2927651842.pdf","grobid_xml":"https://content.openalex.org/works/W2927651842.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1491063910","https://openalex.org/W1540530720","https://openalex.org/W1853158677","https://openalex.org/W1936662467","https://openalex.org/W1985946228","https://openalex.org/W2020598739","https://openalex.org/W2043304335","https://openalex.org/W2060809301","https://openalex.org/W2093591760","https://openalex.org/W2098138211","https://openalex.org/W2101298197","https://openalex.org/W2108101947","https://openalex.org/W2123768455","https://openalex.org/W2127828823","https://openalex.org/W2129020329","https://openalex.org/W2139281871","https://openalex.org/W2139447922","https://openalex.org/W2144357990","https://openalex.org/W2145268834","https://openalex.org/W2154106236","https://openalex.org/W2158714788","https://openalex.org/W2171559274","https://openalex.org/W2284132962","https://openalex.org/W2807724242","https://openalex.org/W2907227701","https://openalex.org/W4238480142"],"related_works":["https://openalex.org/W4386786398","https://openalex.org/W2138293586","https://openalex.org/W2080052720","https://openalex.org/W4319783074","https://openalex.org/W1503179180","https://openalex.org/W4319778501","https://openalex.org/W4255464147","https://openalex.org/W2021797003","https://openalex.org/W4313411469","https://openalex.org/W2151212570"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,91],"ab":[2],"initio":[3],"approaches":[4],"to":[5,15,37,53,71,78,124,221],"protein":[6,59,235,261],"structure":[7,60,70,85,236,262],"prediction":[8,237],"usually":[9,31],"employ":[10],"the":[11,17,22,26,68,73,80,83,88,110,112,115,119,126,142,159,163,167,174,179,199,210,225,228,240,252,267],"Monte":[12,120,154],"Carlo":[13,121,155],"technique":[14],"search":[16,122,276],"structural":[18,164],"conformation":[19,34,248,275],"that":[20,95,223],"has":[21],"lowest":[23,74],"energy.":[24],"However,":[25],"widely-used":[27],"energy":[28,41,56,64,89,97,102,135,149,188,194,230,258],"functions":[29,57,65,136,231,259],"are":[30],"ineffective":[32],"for":[33,58,118,260],"search.":[35,249],"How":[36],"construct":[38,54],"an":[39,192],"effective":[40,55,134,257],"function":[42,98],"remains":[43],"a":[44,51,100,106,147],"challenging":[45],"task.":[46],"RESULTS:":[47],"Here,":[48],"we":[49,76,132,151,177,255],"present":[50,217],"framework":[52,197],"prediction.":[61],"Unlike":[62],"existing":[63],"only":[66],"requiring":[67],"native":[69,84,107,127,143,160,175,211],"be":[72],"one,":[75],"attempt":[77],"maximize":[79],"attraction-basin":[81,113,144,183,201,212],"where":[82],"lies":[86],"in":[87,238],"landscape.":[90],"underlying":[92],"rationale":[93],"is":[94,213],"each":[96],"determines":[99],"specific":[101],"landscape":[103],"together":[104],"with":[105],"attraction-basin,":[108,176],"and":[109,202,245,272],"larger":[111],"is,":[114],"more":[116],"likely":[117],"procedure":[123],"find":[125],"structure.":[128],"Following":[129],"this":[130],"rationale,":[131],"constructed":[133,229,256],"as":[137,277],"follows:":[138],"i)":[139],"To":[140,172],"explore":[141],"determined":[145],"by":[146],"certain":[148],"function,":[150],"performed":[152],"reverse":[153,203],"sampling":[156,204],"starting":[157],"from":[158],"structure,":[161],"identifying":[162],"conformations":[165],"on":[166],"edge":[168,180],"of":[169,182,187,242,269],"attraction-basin.":[170],"ii)":[171],"broaden":[173],"smoothened":[178],"points":[181],"through":[184],"tuning":[185],"weights":[186],"terms,":[189],"thus":[190],"acquiring":[191],"improved":[193],"function.":[195],"Our":[196],"alternates":[198],"broadening":[200],"steps":[205],"(thus":[206],"called":[207],"BARS)":[208],"until":[209],"sufficiently":[214],"large.":[215],"We":[216],"extensive":[218],"experimental":[219],"results":[220],"show":[222],"using":[224],"BARS":[226,253],"framework,":[227,254],"could":[232,265],"greatly":[233],"facilitate":[234],"improving":[239],"quality":[241,268],"predicted":[243,270],"structures":[244,271],"speeding":[246],"up":[247,274],"CONCLUSION:":[250],"Using":[251],"prediction,":[263],"which":[264],"improve":[266],"speed":[273],"well.":[278]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
