Unit

UNIT 1.9 Using the Tools and Resources of the RCSB Protein Data Bank

  1. Shuchismita Dutta1,
  2. Kyle Burkhardt1,
  3. Wolfgang F. Bluhm2,
  4. Helen M. Berman1

Published Online: 1 APR 2005

DOI: 10.1002/0471250953.bi0109s9

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Dutta, S., Burkhardt, K., Bluhm, W. F. and Berman, H. M. 2005. Using the Tools and Resources of the RCSB Protein Data Bank. Current Protocols in Bioinformatics. 1:1.9.

Author Information

  1. 1

    Rutgers University, Piscataway, New Jersey

  2. 2

    University of California, San Diego, La Jolla, California

Publication History

  1. Published Online: 1 APR 2005
  2. Published Print: MAR 2005

This is not the most recent version of the article. View current version (1 DEC 2007)

Abstract

The Protein Data Bank (PDB; http://www.pdb.org) is the world-wide repository for three-dimensional structural data determined using various experimental methods. The options and procedures for searching and downloading structural data from the PDB, which is maintained by the Research Collaboratory for Structural Bioinformatics (RCSB), are described here along with tools for depositing and assessing the quality of structures. Several types of information are associated with each structure deposition including atomic coordinates of the structure, experimental data used to solve the structure, sequences of all macromolecules that constitute the structures, details about the structure solution method, images showing different views of the structure, derived geometric data, and a variety of links to other resources. These data and resources may be used for understanding and designing biochemical, genetic, or other experiments to study the stability or function of the molecule. They can also be used for molecular modeling and drug design.

Keywords:

  • query;
  • validation;
  • deposition;
  • macromolecular structures;
  • proteins;
  • nucleic acids