ASDB：一种利用小分子探测蛋白质功能的资源。

ASDB: a resource for probing protein functions with small molecules.

机构信息

Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.

Department of Pharmacy, Cancer Hospital of Shantou University Medical College, Shantou 515031, China.

出版信息

Bioinformatics. 2016 Jun 1;32(11):1752-4. doi: 10.1093/bioinformatics/btw055. Epub 2016 Jan 28.

DOI:10.1093/bioinformatics/btw055

PMID:26822210

Abstract

UNLABELLED

: Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies. Therefore, we create the Annotated Scaffold Database (ASDB), a computer-readable and systematic target-annotated scaffold database, to serve such needs. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets and medical indications. The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets. The scaffolds consist of 3032 scaffolds derived from drugs and 5163 scaffolds derived from natural products. For given scaffolds, scaffold-target networks can be generated from the database to demonstrate the relations of scaffolds and targets.

AVAILABILITY AND IMPLEMENTATION

ASDB is freely available at http://www.rcdd.org.cn/asdb/with the major web browsers.

CONTACT

junxu@biochemomes.com or xujun9@mail.sysu.edu.cn

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

未标记

：鉴定化学探针或寻找特定生物靶标的支架对于蛋白质功能研究很重要。因此，我们创建了注释支架数据库（ASDB），这是一个计算机可读的、系统的靶标注释支架数据库，以满足这种需求。ASDB 中的支架来源于包括 ChEMBL、DrugBank 和 TCMSP 在内的公共数据库，采用基于支架的分类方法。每个支架都被分配了一个 InChIKey 作为其唯一标识符、能量最小化的 3D 构象和其他计算属性。支架还与药物、天然产物、药物靶点和医学适应症相关联。该数据库可通过文本或结构查询工具进行检索。ASDB 收集了 333601 个支架，与 4368 个靶点相关联。这些支架包括 3032 个源自药物的支架和 5163 个源自天然产物的支架。对于给定的支架，可以从数据库中生成支架-靶标网络，以展示支架和靶标的关系。