3v website

Volume Calculation and Extraction Procedures

3vee is collection of program for the assessment of volumes in protein files.

External Volumes

Volume Calculation

Calculate the volume of a structure for a given probe size

Volume Range

Calculate the volume of a structure for a range probe sizes

Internal Volumes

Channel Finder

Find and extract all major channels from the structure based on their size

Single Channel Extraction

Extract a particular channel with a known x,y,z coordinate

Solvent Extraction

Extract all the solvent volume from a structure

Exit Tunnel Extraction

Calculate the volume of the polypeptide exit tunnel from the 50S ribosomal subunit

Recent runs

Job id: 2015.jul29.5bd PDB id: 1do5  
Program: runVolume

Job id: 2015.jul29.01c PDB id: 1gxa  
Program: runChannelFinder

Job id: 2015.jul29.76a  
Program: runVolumeRange

Job id: 2015.jul28.39b  
Program: runVolumeRange

Job id: 2015.jul28.0af  
Program: runVolume

Job id: 2015.jul28.fb2  
Program: runVolume

'3V: cavity, channel and cleft volume calculator and extractor' (free text)
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562
by Neil R. Voss and Mark Gerstein
Download source code
Site news and updates
If you find this useful or want more functionality please contact Neil <vossman77 [at] yahoo.com>
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