P.R.E.S.S. – An R-package for Exploring Residual-Level Protein Structural Statistics

Date
2012-06-01
Authors
Huang, Yuanyuan
Bonett, Steve
Klockowski, Andrzej
Jernigan, Robert
Wu, Zhijun
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Abstract

P.R.E.S.S. is an R package developed to allow researchers to get access to and manipulate on a large set of statistical data on protein residue-level structural properties such as residue-level virtual bond lengths, virtual bond angles, and virtual torsion angles. A large set of high-resolution protein structures are downloaded and surveyed. Their residue-level structural properties are calculated and documented. The statistical distributions and correlations of these properties can be queried and displayed. Tools are also provided for modeling and analyzing a given structure in terms of its residue-level structural properties. In particular, new tools for computing residue-level statistical potentials and displaying residue-level Ramachandran-like plots are developed for structural analysis and refinement. P.R.E.S.S. will be released in R as an open source software package, with a user-friendly GUI, accessible and executable by a public user in any R environment.

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This is a manuscript of an Electronic version of an article published as Journal of Bioinformatics and Computational Biology 10, no. 03 (2012): 1242007, DOI: 10.1142/S0219720012420073. © copyright World Scientific Publishing Company, http://www.worldscientific.com/worldscinet/jbcb.

Keywords
Protein structure analysis, protein residual-level structural properties, structural bioinformatics, statistical potentials, structural correlation plots
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