Zhihong Liu1, Peng Ding1, Xin Yan1, Minghao Zheng2, Huihao Zhou1, Yuehua Xu1, Yunfei Du3, Qiong Gu1, Jun Xu1. 1. Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China. 2. Department of Pharmacy, Cancer Hospital of Shantou University Medical College, Shantou 515031, China. 3. National University of Defense Technology, National Supercomupter Center in Guangzhou, Sun Yat-sen University, Guangzhou 510006, China.
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.
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.