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Nucleic Acids Research Advance Access originally published online on December 6, 2006
Nucleic Acids Research 2007 35(Database issue):D202-D207; doi:10.1093/nar/gkl802
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Nucleic Acids Research, 2007, Vol. 35, Database issue D202-D207
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PIDD: database for Protein Inter-atomic Distance Distributions

Di Wu, Feng Cui, Robert Jernigan1 and Zhijun Wu2,*

Program on Bioinformatics and Computational Biology, Biophysics, and Molecular Biology, Iowa State University Ames, IA 50011, USA 1 Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University Ames, IA 50011, USA 2 Department of Mathematics, Iowa State University Ames, IA 50011, USA

*To whom correspondence should be addressed. Tel: +1 515 294 8165; Fax: +1 515 294 5454; Email: zhijun{at}iastate.edu

Received March 31, 2006. Revised September 26, 2006. Accepted September 29, 2006.

Protein Inter-atomic Distance Distributions (PIDD) is a dedicated database and structural bio-informatics system for distance based protein modeling. The database is developed to host and analyze the statistical data for protein inter-atomic distances based on their distributions in databases of known protein structures such as in the Protein Data Bank (PDB). PIDD is capable of generating, caching, and displaying the statistical distributions of the distances of various types and ranges. The collected information can be used to extract geometric restraints or mean-force potentials for protein structure determination including nuclear magnetic resonance structure determination and comparative model refinement. PIDD is supported with a friendly designed web interface so that users can easily specify the distance types and ranges, and retrieve, visualize or download the distributions of the distances as they desire. PIDD is freely accessible at http://www.math.iastate.edu/pidd


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