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Identification of Small Molecule-binding Proteins in a Native Cellular Environment by Live-cell Photoaffinity Labeling
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ASDB: a resource for probing protein functions with small molecules.

Zhihong Liu1, Peng Ding1, Xin Yan1

  • 1Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.

Bioinformatics (Oxford, England)
|January 30, 2016
PubMed
Summary

The Annotated Scaffold Database (ASDB) provides a comprehensive resource for identifying chemical scaffolds linked to biological targets, aiding drug discovery and protein function studies. It systematically organizes over 333,000 scaffolds with associated targets, drugs, and natural products.

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Area of Science:

  • * Cheminformatics and Computational Biology
  • * Drug Discovery and Development
  • * Structural Biology

Background:

  • * Identifying chemical probes and molecular scaffolds is crucial for understanding protein function and advancing drug discovery.
  • * Existing resources may lack systematic annotation or comprehensive scaffold-target relationships.
  • * A need exists for a structured, searchable database of chemical scaffolds linked to biological targets.

Purpose of the Study:

  • * To develop and present the Annotated Scaffold Database (ASDB), a systematic, target-annotated scaffold database.
  • * To facilitate the identification of chemical probes and scaffolds for specific biological targets.
  • * To provide a resource for exploring scaffold-target relationships in drug discovery and biological research.

Main Methods:

  • * Scaffolds were systematically extracted from public databases (ChEMBL, DrugBank, TCMSP) using a scaffold-based classification approach.
  • * Each scaffold was assigned a unique InChIKey, energy-minimized 3D conformations, and calculated properties.
  • * The database integrates scaffold information with associated drugs, natural products, targets, and medical indications.

Main Results:

  • * ASDB contains 333,601 scaffolds, linked to 4,368 targets.
  • * Includes 3,032 scaffolds derived from drugs and 5,163 from natural products.
  • * Enables generation of scaffold-target networks to visualize relationships.

Conclusions:

  • * ASDB serves as a valuable, computer-readable resource for researchers in drug discovery and chemical biology.
  • * The database facilitates the exploration of chemical space and target interactions.
  • * ASDB is freely accessible, promoting wider research and discovery.