NucProt Parameter Set Traditionally, for biomolecular packing calculations research has focused on proteins. Besides proteins, RNA is the other large biomolecule that has tertiary structure interactions and complex packing. No one has yet quantitatively investigated RNA packing or compared its packing to that of proteins because, until recently, there were no large RNA structures. Here we address this question in detail, using Voronoi volume calculations on a set of high-resolution RNA crystal structures. [ Citation info | Packing-Eff Online! ]

The Voronoi Construction NucProt Parameters Volume Data Files Standard Volumes RNA and Protein Residue Volumes RNA Atom Volumes Protein Atom Volumes Packing-Eff Online! (NEW) PSV and Volume Calculator the 3V Contact Volume Calculator (beta) Extended Standard Volume DAT files [ Standard Method | Radical Plane | No Crystal Symm ] Volume Distributions Old Parameter Sets for Geometry Programs Downloadable Software Raw Data Protein Geometry Library v2.3.1 (README) Standard Source: libproteingeometry-2.3.1.tgz Required Program Files Standard Volumes Atom Definitions Residue Definitions List of PDB files used RNA PDB Files Protein PDB Files Merged Raw RNA Volume Data (gzipped) Standard Set: standard.out.gz Radical Plane: radical.out.gz No Crystal Symm: nosymm.out.gz Individual Volume Out Files (tar/gzipped) [ Standard | Radical | NoSymm ] Grouped Volume Out Files (gzipped) disjoint: [ tRNA | SRP RNA | Small RNA | Small rRNA | Ribosomes ] extra: [ RNA only | High Resolution ] ProtOr Raw Volume Data: protor.out.gz

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Copyright 1995-2003, M. Gerstein and others
Email: Mark.Gerstein@yale.edu
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Last modified by Neil Voss on Feb 3, 2005