RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.
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DOI：
10.1093/nar/gkac1077
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发表时间：
2023-01-06
影响因子：
14.9
通讯作者：
Zardecki, Christine
中科院分区：
文献类型：
--
作者：
Burley, Stephen K.;Bhikadiya, Charmi;Bi, Chunxiao;Bittrich, Sebastian;Chao, Henry;Chen, Li;Craig, Paul A.;Crichlow, Gregg, V;Dalenberg, Kenneth;Duarte, Jose M.;Dutta, Shuchismita;Fayazi, Maryam;Feng, Zukang;Flatt, Justin W.;Ganesan, Sai;Ghosh, Sutapa;Goodsell, David S.;Green, Rachel Kramer;Guranovic, Vladimir;Henry, Jeremy;Hudson, Brian P.;Khokhriakov, Igor;Lawson, Catherine L.;Liang, Yuhe;Lowe, Robert;Peisach, Ezra;Persikova, Irina;Piehl, Dennis W.;Rose, Yana;Sali, Andrej;Segura, Joan;Sekharan, Monica;Shao, Chenghua;Vallat, Brinda;Voigt, Maria;Webb, Ben;Westbrook, John D.;Whetstone, Shamara;Young, Jasmine Y.;Zalevsky, Arthur;Zardecki, Christine
结构生物信息学蛋白质数据库研究合作实验室(RCSB PDB)是世界蛋白质数据库(WWPDB)的创始成员，是开放访问PDB档案的美国数据中心。作为WWPDB指定的档案保管员，RCSB PDB还负责PDB数据的安全。每年，RCSB PDB为在所有永久居住的大陆上工作的10,000名三维(3D)生物结构的储户提供服务。RCSB PDB从其专注于研究的RCSB.org门户网站向几乎每个联合国承认的国家、地区等的数百万PDB数据消费者提供数据。这期数据库贡献描述了以研究为重点的RCSB.org门户网站的升级，该门户网站创建了一站式商店，开放获取∼20万个实验确定的生物大分子PDB结构以及使用人工智能/机器学习方法预测的1000个合并的计算结构模型(CSM)。RCSB.org是一个“活的数据资源”。每个PDB结构和CSM每周都与来自外部生物数据资源的相关功能注释集成在一起，为RCSB.org上免费提供的整个3D BioStructure数据语料库提供最新信息，没有使用限制。在RCSB.org中，PDB结构和CSMS的来源和可靠性都得到了明确的确认。两者都是完全可搜索的，并且可以使用完整的RCSB.org门户功能进行分析和可视化。.org现在提供了∼200000个实验确定的PDB结构，以及1M个计算结构模型，所有这些模型都可以使用自定义工具和功能进行搜索、分析、可视化和探索。
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities. RCSB.org now delivers ∼200 000 experimentally-determined PDB structures alongside >1M Computed Structure Models that can all be searched, analyzed, visualized, and explored using custom tools and features.
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影响因子：
14.9
作者：
Blum M;Chang HY;Chuguransky S;Grego T;Kandasaamy S;Mitchell A;Nuka G;Paysan-Lafosse T;Qureshi M;Raj S;Richardson L;Salazar GA;Williams L;Bork P;Bridge A;Gough J;Haft DH;Letunic I;Marchler-Bauer A;Mi H;Natale DA;Necci M;Orengo CA;Pandurangan AP;Rivoire C;Sigrist CJA;Sillitoe I;Thanki N;Thomas PD;Tosatto SCE;Wu CH;Bateman A;Finn RD
通讯作者：
Finn RD
影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
14.9
作者：
wwPDB consortium
通讯作者：
wwPDB consortium
DOI：
10.1016/j.str.2021.04.010
发表时间：
2021-06-03
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
Burley SK;Berman HM
通讯作者：
Berman HM
影响因子：
3.4
作者：
BERMAN, HM;OLSON, WK;SCHNEIDER, B
通讯作者：
SCHNEIDER, B