VOLUME CALCULATION WEB TOOLS
XYZR example files
the 3V Volume Calculator
the 3V Channel Extractor
- Download the source code: 3v, v1.2 (.tgz)
released on June 2, 2009
- Cavity Extractor — extracts the cavities for a given probe radius
- Channel Extractor — extracts a particular channel from the solvent
- FSV Calculator — calculates the Fractional Solvent Volume
- Solvent Extractor — extracts the all of the solvent
- Tunnel Extractor — extracts the ribosomal exit tunnel from the H. marismortui structure
- VDW Calculator — calculate the van der Waals volume and surface area
- Volume Calculator — calculate the volume and surface area for any probe radius
- NR Voss, M Gerstein, TA Steitz, PB Moore.
"The geometry of the ribosomal polypeptide exit tunnel."
J Mol Biol. v360 (4): 2006, pp. 893-906.
Pubmed ID: 16784753
- NR Voss
"Geometric Studies of RNA and Ribosomes, and Ribosome
PhD dissertation, Yale University, 2007