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Related Experiment Videos

The PDBbind database: methodologies and updates.

Renxiao Wang1, Xueliang Fang, Yipin Lu

  • 1Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, 48109-0934, USA.

Journal of Medicinal Chemistry
|June 10, 2005
PubMed
Summary
This summary is machine-generated.

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The PDBbind database now offers version 2003, a comprehensive resource for protein-ligand binding affinities. This updated collection is valuable for computational studies like molecular docking and scoring.

Area of Science:

  • Biochemistry and Structural Biology
  • Computational Chemistry
  • Bioinformatics

Background:

  • The Protein Data Bank (PDB) is a primary repository for structural data of biomolecules.
  • Understanding protein-ligand interactions is crucial for drug discovery and molecular biology.
  • Accurate binding affinity data is essential for validating computational models.

Purpose of the Study:

  • To present the latest version (2003) of the PDBbind database.
  • To provide a curated collection of binding affinities for protein-ligand complexes.
  • To establish a refined dataset for computational studies.

Main Methods:

  • Identification of protein-ligand complexes from the Protein Data Bank (PDB).
  • Retrieval and curation of experimentally determined binding affinities (Kd, Ki, IC50).

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  • Selection of a high-quality 'refined set' for computational benchmarking.

    • Main Results:

    • Version 2003 of PDBbind includes data from PDB release 107 (January 2004).
    • 5897 entries were identified as protein-ligand complexes.
    • Binding affinities were compiled for 1622 complexes, with 900 selected for the refined set.

    Conclusions:

    • The PDBbind database (version 2003) is a valuable, up-to-date resource for protein-ligand binding data.
    • The refined set provides a reliable benchmark for docking and scoring algorithms.
    • The database is accessible online, facilitating research in structural biology and drug discovery.