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CRESTANO - Common REst api for Structural ANnotation

CRESTANO - 用于结构注释的通用 REst api

基本信息

批准号：
BB/K016970/1
负责人：
Gerard Kleywegt
金额：
$ 14.99万
依托单位：
European Bioinformatics Institute
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2013
资助国家：
英国
起止时间：
2013 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FK016970%2F1
关键词：
CRESTANO Common REst api Structural

项目摘要

The Protein Data Bank in Europe (PDBe; pdbe.org) is one of the core resources at the European Bioinformatics Institute (EMBL-EBI). PDBe is a founding member of the Worldwide Protein Data Bank (wwPDB), which manages the PDB, the single global archive of biomacromolecular structure data. The other wwPDB partners are RCSB, PDBj and BMRB. PDBe has operated a deposition and annotation facility for PDB data since 1998. Over the years, PDBe has developed advanced tools and services for analysis of biomacromolecules (including unique tools such as PDBeFold, PDBePISA and PDBeMotif) and for delivery of PDB data to the user community. In addition, PDBe develops and maintains critical resources such as SIFTS (Structure Integration with Function, Taxonomy and Sequences), a vital source of up-to-date cross-reference information to other biological data resources.The Cambridge Crystallographic Data Centre (CCDC; www.ccdc.cam.ac.uk) manages the Cambridge Structural Database (CSD), the main archive for small-molecule crystal structure data. CSD contains structural data for organic and organometallic compounds obtained using single crystal X-ray and neutron diffraction methods or based on powder diffraction data. The archive was established in 1965 and now contains more than 600,000 structures of small molecules. In addition to archiving the small molecule structural data, CCDC has developed many tools for the analysis of these data.The information available in the PDB archive is used by structural biologists and the wider biomedical community to understand the structures archived in the PDB, while CSD data amongst many other applications can be used by chemists and biochemists for automatic screening of natural molecules suitable as drug candidates. Recently, to improve the annotation and validation of small molecule information in the PDB, wwPDB has entered into a collaboration with CCDC. As part of this, CCDC has made a number of tools available to the wwPDB partners, including Mogul, which will be used for validation of small molecule geometry during deposition and annotation of PDB data. This will constitute a major improvement as analysis of ligand structures in the PDB has shown that the majority of ligand models can be improved. The structure validation pipeline, which includes Mogul and which will become a critical part of the new wwPDB Deposition and Annotation system (D&A), is being developed at PDBe.The goal of the present project is to implement a web-services API that will provide access to biomacromolecular structure data and advanced analyses and annotations of those structures available from PDBe. Additionally, CCDC will develop infrastructure to allow access to small-molecule data in the Cambridge Structural Database (CSD) for those compounds that are present in the both the CSD and the PDB. This will facilitate real-time programmatic access to up-to-date information from PDBe databases and advanced tools and services, which will become available to any bioinformatics and structural-biology-workflow systems as well as individual programs. In addition, access to experimentally determined structures from the CSD will provide better quality starting models for ligands during the macromolecular structure determination process. This, in turn, will improve the quality of deposited ligand data in the PDB, benefitting chemoinformatics research and informing the structure-based design of new drugs.In this project, we propose to develop a method to provide access to types of PDBe and CCDC data and information in an integrated framework:1. PDB data from the PDBe database infrastructure2. Advanced analysis and annotations on biomacromolecular assemblies3. Ligand environment and 3D structural motifs data from PDBeMotif4. Up-to-date cross-references for all PDB entries, taken from the SIFTS resource5. Data-quality indicators for all PDB entries6. Access to CSD data for molecules that are also in the PDB

欧洲蛋白质数据库（PDBe; pdbe.org）是欧洲生物信息学研究所（EMBL-EBI）的核心资源之一。PDBe是全球蛋白质数据库（wwPDB）的创始成员，该数据库管理PDB，生物大分子结构数据的单一全球存档。wwPDB的其他合作伙伴是RCSB、PDBj和BMRB。自1998年以来，PDBe一直在为PDB数据提供沉积和注释设施。多年来，PDBe开发了用于分析生物大分子的先进工具和服务（包括PDBeFold，PDBePISA和PDBeMotif等独特工具），并将PDB数据交付给用户社区。此外，PDBe还开发和维护重要的资源，如SIFTS（结构与功能、分类和序列的整合），这是与其他生物数据资源交叉引用的最新信息的重要来源。剑桥晶体数据中心（CCDC; www.ccdc.cam.ac.uk）管理着剑桥结构数据库（CSD），这是小分子晶体结构数据的主要存档。CSD包含使用单晶X射线和中子衍射方法或基于粉末衍射数据获得的有机和有机金属化合物的结构数据。该档案馆成立于1965年，现在包含超过60万个小分子结构。除了存档小分子结构数据外，CCDC还开发了许多用于分析这些数据的工具。PDB存档中的可用信息被结构生物学家和更广泛的生物医学界用于了解PDB中存档的结构，而CSD数据以及许多其他应用程序可被化学家和生物化学家用于自动筛选适合作为候选药物的天然分子。最近，为了改进PDB中小分子信息的注释和验证，wwPDB与CCDC进行了合作。作为其中的一部分，CCDC向wwPDB合作伙伴提供了许多工具，包括Mogul，这些工具将用于在沉积和注释PDB数据期间验证小分子几何形状。这将构成一个重大的改进，因为PDB中的配体结构分析表明，大多数配体模型可以得到改进。PDBe正在开发包括Mogul在内的结构验证管道，该管道将成为新的wwPDB沉积和注释系统（D&A）的关键部分。本项目的目标是实现一个Web服务API，该API将提供对生物大分子结构数据的访问以及对PDBe提供的这些结构的高级分析和注释。此外，CCDC还将开发基础设施，以便访问剑桥结构数据库（CSD）中存在于CSD和PDB中的化合物的小分子数据。这将有助于实时编程访问PDBe数据库和高级工具和服务中的最新信息，这些信息将可用于任何生物信息学和结构生物学工作流程系统以及单个程序。此外，从CSD获得实验确定的结构将在大分子结构确定过程期间为配体提供更好质量的起始模型。这反过来又将提高PDB中沉积的配体数据的质量，有利于化学信息学研究，并为基于结构的新药设计提供信息。在本项目中，我们提出开发一种方法，在一个集成的框架中提供对PDBe和CCDC数据和信息类型的访问：1.来自PDBe数据库基础设施的PDB数据2.生物大分子结构的高级分析和注释3。来自PDBeMotif 4的配体环境和3D结构基序数据。所有PDB条目的最新交叉引用，取自SIFTS资源5。所有PDB条目的数据质量指标6.访问PDB中的分子的CSD数据

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.

DOI：
10.1002/bip.22434
发表时间：
2014-06
期刊：
BIOPOLYMERS
影响因子：
2.9
作者：
Dutta, Shuchismita;Dimitropoulos, Dimitris;Feng, Zukang;Persikova, Irina;Sen, Sanchayita;Shao, Chenghua;Westbrook, John;Young, Jasmine;Zhuravleva, Marina A.;Kleywegt, Gerard J.;Berman, Helen M.
通讯作者：
Berman, Helen M.

How community has shaped the Protein Data Bank.

DOI：
10.1016/j.str.2013.07.010
发表时间：
2013-09-03
期刊：
STRUCTURE
影响因子：
5.7
作者：
Berman, Helen M.;Kleywegt, Gerard J.;Nakamura, Haruki;Markley, John L.
通讯作者：
Markley, John L.

The Protein Data Bank archive as an open data resource.

DOI：
10.1007/s10822-014-9770-y
发表时间：
2014-10
期刊：
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
影响因子：
3.5
作者：
Berman, Helen M.;Kleywegt, Gerard J.;Nakamura, Haruki;Markley, John L.
通讯作者：
Markley, John L.

Small molecule annotation for the Protein Data Bank.

DOI：
10.1093/database/bau116
发表时间：
2014
期刊：
Database : the journal of biological databases and curation
影响因子：
0
作者：
Sen S;Young J;Berrisford JM;Chen M;Conroy MJ;Dutta S;Di Costanzo L;Gao G;Ghosh S;Hudson BP;Igarashi R;Kengaku Y;Liang Y;Peisach E;Persikova I;Mukhopadhyay A;Narayanan BC;Sahni G;Sato J;Sekharan M;Shao C;Tan L;Zhuravleva MA
通讯作者：
Zhuravleva MA

The role of structural bioinformatics resources in the era of integrative structural biology.