Unit

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

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

Published Online: 1 DEC 2007

DOI: 10.1002/0471250953.bi0109s20

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Dutta, S., M. Berman, H. and F. Bluhm, W. 2007. Using the Tools and Resources of the RCSB Protein Data Bank. Current Protocols in Bioinformatics. 20:1.9:1.9.1–1.9.24.

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 DEC 2007
  2. Published Print: 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 Research Collaboratory for Structural Bioinformatics (RCSB) PDB are described here, along with tools for 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 it, sequences of all macromolecules in 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 the function and stability of the molecule and for designing biochemical, genetic, or other experiments. They can also be used for molecular modeling and drug design. Curr. Protoc. Bioinform. 20:1.9.1-1.9.24. © 2007 by John Wiley & Sons, Inc.

Keywords:

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