PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS

结构生物信息学研究合作实验室的 PDB 管理

• 批准号: 10702253
• 负责人: STEPHEN K BURLEY
• 金额: $ 80万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10702253
• 关键词: 3-Dimensional; Administrative Supplement; Advocate; Award; Bioinformatics; Biology; Certification; Data; Development; Doctor of Medicine; Environment; FAIR principles; Funding; Modeling; Movement; National Institute of General Medical Sciences; Outcome; Parents; Positioning Attribute; Principal Investigator; Proteins; Reporting; Research; Role; Secure; Services; Structural Models; Structure; TRUST principles; Testing; United States National Institutes of Health; Work; collaboratory; data repository; digital; protein data bank; public trust; response; web portal

Administrative Supplement Request in Response to PA-20-272 Parent Award Identifier: 1R01GM133198 Parent Award Title: PDB Management by the Research Collaboratory for Structural Bioinformatics Parent Award Principal Investigator: Stephen K. Burley, M.D., D.Phil. Supplement Request: Scaling of RCSB PDB Backend and Frontend Services for RCSB.org Project Summary/Abstract: In its role as a core NIH data repository, the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is committed to the best practices articulated by the FAIR and TRUST principles. Established in 1971 as the first open-access digital data repository in biology, the PDB has been a leading exemplar of FAIR and a pioneer in the open access movement. RCSB PDB was an early adopter in securing CoreTrustSeal certification and advocating publicly for the TRUST principles. In this supplement application, funds are requested to support scaling of RCSB PDB research-focused RCSB.org web portal Backend and Frontend Services by two orders of magnitude for delivery of ~200 million Computed Structure Models (CSMs) from AlphaFoldDB and the ModelArchive alongside all of the experimentally-determined structures stored in the PDB. Parallel delivery of CSMs with PDB data will enable many millions of RCSB.org users worldwide to analyze, visualize, and explore predicted 3D structural models for nearly every protein represented within UniProt (fully integrated with ~200,000 PDB structures).

回应PA-20-272的行政补充请求

项目成果

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals

• DOI: 10.1016/j.str.2018.11.007
• 发表时间: 2019-02-05
• 期刊: STRUCTURE
• 影响因子: 5.7
• 作者: Westbrook, John D.;Burley, Stephen K.
• 通讯作者: Burley, Stephen K.

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.

• DOI: 10.1093/nar/gkab314
• 发表时间: 2021-07-02
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Sehnal D;Bittrich S;Deshpande M;Svobodová R;Berka K;Bazgier V;Velankar S;Burley SK;Koča J;Rose AS
• 通讯作者: Rose AS

Real-time structural motif searching in proteins using an inverted index strategy.

使用倒数索引策略在蛋白质中进行实时结构基序搜索。

• DOI: 10.1371/journal.pcbi.1008502
• 发表时间: 2020-12
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Bittrich S;Burley SK;Rose AS
• 通讯作者: Rose AS

RCSB Protein Data Bank 1D tools and services.

• DOI: 10.1093/bioinformatics/btaa1012
• 发表时间: 2021-04-01
• 期刊: Bioinformatics (Oxford, England)
• 作者: Segura J;Rose Y;Westbrook J;Burley SK;Duarte JM
• 通讯作者: Duarte JM

Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site Diversity.

冠状病毒主要蛋白酶活性位点多样性的生物信息学和 3D 结构分析。

• 发表时间: 2022
• 期刊: FASEB journal : official publication of the Federation of American Societies for Experimental Biology
• 作者: WuWu,Amy;Lubin,JosephH;Olivas,Cassandra;Zardecki,Christine;Balogun,MaryAgnes;Bacorn,MickaylaL;Khare,SagarD;Burley,StephenK
• 通讯作者: Burley,StephenK