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: 2019.apr19.305 PDB id: 5heb  
Program: runVolume


Job id: 2019.apr19.e9a  
Program: runChannelFinder


Job id: 2019.apr19.bda  
Program: runVolume


Job id: 2019.apr18.df5  
Program: runChannelFinder


Job id: 2019.apr18.c32  
Program: runVolume


Job id: 2019.apr18.c22 PDB id: 1LFH  
Program: runVolume


Citation:
'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
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If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
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