{"id":"https://openalex.org/W4225774159","doi":"https://doi.org/10.1186/s12859-022-04595-0","title":"D3PM: a comprehensive database for protein motions ranging from residue to domain","display_name":"D3PM: a comprehensive database for protein motions ranging from residue to domain","publication_year":2022,"publication_date":"2022-02-14","ids":{"openalex":"https://openalex.org/W4225774159","doi":"https://doi.org/10.1186/s12859-022-04595-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/35164668"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04595-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04595-0","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-022-04595-0.pdf","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://link.springer.com/content/pdf/10.1186/s12859-022-04595-0.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100346430","display_name":"Cheng Peng","orcid":"https://orcid.org/0000-0001-6233-6974"},"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/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"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":"Cheng Peng","raw_affiliation_strings":["CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China","University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110352412","display_name":"Xinben Zhang","orcid":null},"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/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinben Zhang","raw_affiliation_strings":["CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083748084","display_name":"Zhijian Xu","orcid":"https://orcid.org/0000-0002-3063-8473"},"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/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"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":"Zhijian Xu","raw_affiliation_strings":["CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China. zjxu@simm.ac.cn","University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China. zjxu@simm.ac.cn","CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China. zjxu@simm.ac.cn","institution_ids":["https://openalex.org/I4210112820"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China. zjxu@simm.ac.cn","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103285098","display_name":"Zhaoqiang Chen","orcid":"https://orcid.org/0000-0002-8847-7545"},"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/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaoqiang Chen","raw_affiliation_strings":["CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100674982","display_name":"Yanqing Yang","orcid":"https://orcid.org/0009-0001-3252-9756"},"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/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"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":"Yanqing Yang","raw_affiliation_strings":["CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China","University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102832964","display_name":"Tingting Cai","orcid":"https://orcid.org/0009-0006-0847-8051"},"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/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tingting Cai","raw_affiliation_strings":["CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059083216","display_name":"Weiliang Zhu","orcid":"https://orcid.org/0000-0001-6699-5299"},"institutions":[{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210113896","display_name":"Qingdao National Laboratory for Marine Science and Technology","ror":"https://ror.org/026sv7t11","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210113896"]},{"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":"Weiliang Zhu","raw_affiliation_strings":["CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China. wlzhu@simm.ac.cn","Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao, 266237, People's Republic of China. wlzhu@simm.ac.cn","University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China. wlzhu@simm.ac.cn","University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China"],"raw_orcid":"https://orcid.org/0000-0001-6699-5299","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, People's Republic of China. wlzhu@simm.ac.cn","institution_ids":["https://openalex.org/I4210112820"]},{"raw_affiliation_string":"Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao, 266237, People's Republic of China. wlzhu@simm.ac.cn","institution_ids":["https://openalex.org/I4210113896"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China. wlzhu@simm.ac.cn","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5059083216","https://openalex.org/A5083748084"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820","https://openalex.org/I4210113896","https://openalex.org/I4210165038"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.0073,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.73657349,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"1","first_page":"70","last_page":"70"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8607000112533569,"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":0.8607000112533569,"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/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.0421999990940094,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.01590000092983246,"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/residue","display_name":"Residue (chemistry)","score":0.6566146016120911},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5940626263618469},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5257245898246765},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.510071337223053},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.4611421525478363},{"id":"https://openalex.org/keywords/amino-acid-residue","display_name":"Amino acid residue","score":0.46042394638061523},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4603329598903656},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.44562143087387085},{"id":"https://openalex.org/keywords/binding-domain","display_name":"Binding domain","score":0.4440135657787323},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.44321560859680176},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.43359896540641785},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.431432843208313},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30411797761917114},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.29864636063575745},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2838663160800934}],"concepts":[{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.6566146016120911},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5940626263618469},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5257245898246765},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.510071337223053},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.4611421525478363},{"id":"https://openalex.org/C2994376932","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Amino acid residue","level":4,"score":0.46042394638061523},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4603329598903656},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.44562143087387085},{"id":"https://openalex.org/C25166345","wikidata":"https://www.wikidata.org/wiki/Q4914012","display_name":"Binding domain","level":3,"score":0.4440135657787323},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.44321560859680176},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.43359896540641785},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.431432843208313},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30411797761917114},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.29864636063575745},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2838663160800934},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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/s12859-022-04595-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04595-0","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-022-04595-0.pdf","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:35164668","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35164668","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:98bbd7169d9745079041b1806609e68d","is_oa":true,"landing_page_url":"https://doaj.org/article/98bbd7169d9745079041b1806609e68d","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 23, Iss 1, Pp 1-11 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8845362","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8845362","pdf_url":null,"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"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04595-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04595-0","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-022-04595-0.pdf","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/G4363245776","display_name":null,"funder_award_id":"2018ZX09711002","funder_id":"https://openalex.org/F4320336020","funder_display_name":"National Key New Drug Creation and Manufacturing Program, Ministry of Science and Technology"},{"id":"https://openalex.org/G6206163954","display_name":null,"funder_award_id":"2016YFA0502301","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6387123747","display_name":null,"funder_award_id":"2018ZX09711002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6793415282","display_name":null,"funder_award_id":"81872797","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7473496705","display_name":null,"funder_award_id":"2018ZX09711002","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320336020","display_name":"National Key New Drug Creation and Manufacturing Program, Ministry of Science and Technology","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4225774159.pdf","grobid_xml":"https://content.openalex.org/works/W4225774159.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1516459493","https://openalex.org/W1544837431","https://openalex.org/W1801976355","https://openalex.org/W1974645077","https://openalex.org/W1997172276","https://openalex.org/W1997892597","https://openalex.org/W1998412941","https://openalex.org/W2002733813","https://openalex.org/W2005132559","https://openalex.org/W2005817231","https://openalex.org/W2012268513","https://openalex.org/W2015771185","https://openalex.org/W2016088798","https://openalex.org/W2018507678","https://openalex.org/W2022402206","https://openalex.org/W2025895105","https://openalex.org/W2027126729","https://openalex.org/W2038019215","https://openalex.org/W2049888624","https://openalex.org/W2070701334","https://openalex.org/W2076812385","https://openalex.org/W2085227451","https://openalex.org/W2091326717","https://openalex.org/W2093221728","https://openalex.org/W2104398328","https://openalex.org/W2105900919","https://openalex.org/W2119613595","https://openalex.org/W2122326469","https://openalex.org/W2133671332","https://openalex.org/W2134967712","https://openalex.org/W2140940323","https://openalex.org/W2149301682","https://openalex.org/W2149796727","https://openalex.org/W2159275700","https://openalex.org/W2166905169","https://openalex.org/W2168822029","https://openalex.org/W2178096376","https://openalex.org/W2253505504","https://openalex.org/W2315174892","https://openalex.org/W2331455101","https://openalex.org/W2343614482","https://openalex.org/W2467625524","https://openalex.org/W2767649956","https://openalex.org/W2767891136"],"related_works":["https://openalex.org/W3165639034","https://openalex.org/W2042694939","https://openalex.org/W2048464673","https://openalex.org/W4299020419","https://openalex.org/W2950723525","https://openalex.org/W1984695931","https://openalex.org/W1967174599","https://openalex.org/W4210400031","https://openalex.org/W2462757626","https://openalex.org/W1546756166"],"abstract_inverted_index":{"BACKGROUND:":[0],"Knowledge":[1],"of":[2,75,89,95,124,131,142,158],"protein":[3,16,53,61,76,79,143,159,217,231,236],"motions":[4,17,80,94,108,218,232],"is":[5,27,212,243],"significant":[6,162],"to":[7,71,91,222],"understand":[8],"its":[9],"functions.":[10],"While":[11],"currently":[12],"available":[13,244],"databases":[14],"for":[15,204,228,234],"are":[18,119,174],"mostly":[19],"focused":[20],"on":[21,29,184,245],"overall":[22,86,107,125,147],"domain":[23],"motions,":[24,41],"little":[25],"attention":[26],"paid":[28],"local":[30,39,92],"residue":[31,40,114,133,186,221],"motions.":[32,77,115,134],"Albeit":[33],"with":[34,106,112],"relatively":[35],"small":[36],"scale,":[37],"the":[38,73,82,100,185],"especially":[42],"those":[43],"residues":[44],"in":[45,52,68,81,165,188],"binding":[46,96,167,181,189],"pockets,":[47],"may":[48],"play":[49],"crucial":[50],"roles":[51],"functioning":[54],"and":[55,109,128,176,197,207,233,238],"ligands":[56],"binding.":[57],"RESULTS:":[58],"A":[59],"comprehensive":[60,214],"motion":[62,117],"database,":[63],"namely":[64],"D3PM,":[65],"was":[66],"constructed":[67],"this":[69],"study":[70],"facilitate":[72],"analysis":[74],"The":[78,116,241],"D3PM":[83,101,211,242],"range":[84],"from":[85,220],"structural":[87,126,163],"changes":[88,127,164,173],"macromolecule":[90],"flip":[93],"pocket":[97,113,132,205],"residues.":[98],"Currently,":[99],"has":[102],"collected":[103],"7679":[104],"proteins":[105,111],"3513":[110],"patterns":[118],"classified":[120,192],"into":[121,195],"4":[122],"types":[123,130],"5":[129],"Impressively,":[135],"we":[136,191],"found":[137],"that":[138,170],"less":[139],"than":[140,156],"15%":[141],"pairs":[144,160],"have":[145,161],"obvious":[146],"conformational":[148,172],"adaptations":[149],"induced":[150],"by":[151],"ligand":[152,166,180],"binding,":[153],"while":[154],"more":[155],"50%":[157],"sites,":[168],"indicating":[169],"ligand-induced":[171],"drastic":[175],"mainly":[177],"confined":[178],"around":[179],"sites.":[182],"Based":[183],"preference":[187],"pocket,":[190],"amino":[193],"acids":[194],"\"pocketphilic\"":[196],"\"pocketphobic\"":[198],"residues,":[199],"which":[200,224],"should":[201,225],"be":[202,226],"helpful":[203],"prediction":[206],"drug":[208,239],"design.":[209,240],"CONCLUSION:":[210],"a":[213],"database":[215],"about":[216],"ranging":[219],"domain,":[223],"useful":[227],"exploring":[229],"diverse":[230],"understanding":[235],"function":[237],"www.d3pharma.com/D3PM/index.php":[246],".":[247]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}