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.mar29.d5c  
Program: runVolume

Job id: 2015.mar28.694 PDB id: 3g5u  
Program: runChannelFinder

Job id: 2015.mar28.e5b  
Program: runVolume

Job id: 2015.mar28.c9f  
Program: runVolume

Job id: 2015.mar27.c85 PDB id: 1F16  
Program: runSolvent

Job id: 2015.mar27.afb PDB id: 1f16  
Program: runSolvent

'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
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If you find this useful or want more functionality please contact Neil <vossman77 [at] yahoo.com>
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