Title: PRTAD: A database for protein residue torsion angle distributions

Authors: Xiaoyong Sun, Di Wu, Robert Jernigan, Zhijun Wu

Addresses: Program on Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa 50011, USA. ' Department of Mathematics, Western Kentucky University, Bowling Green, Kentucky 42101, USA. ' Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA. ' Department of Mathematics, Iowa State University, Ames, Iowa 50011, USA

Abstract: PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modelling. The database is developed to host and analyse the statistical data for protein residue level |virtual| bond and torsion angles obtained from their distributions in databases of known protein structures such as in the PDB Data Bank. PRTAD is capable of generating, caching, and displaying the statistical distributions of the angles of various types. The collected information can be used to extract geometric restraints or define statistical potentials for protein structure determination. PRTAD is supported with a friendly designed web interface so that users can easily specify the angle types, and retrieve, visualise, or download the distributions of the angles as they desire.

Keywords: protein structural databases; structural refinement; structural analysis; protein geometric properties; virtual bond lengths; virtual bond angles; statistical potentials; bioinformatics; protein residue; torsion angle distributions; protein analysis; modelling; web interface.

DOI: 10.1504/IJDMB.2009.029207

International Journal of Data Mining and Bioinformatics, 2009 Vol.3 No.4, pp.469 - 482

Published online: 09 Nov 2009 *

Full-text access for editors Access for subscribers Purchase this article Comment on this article