From: Seweryn Bialasiewicz (
Date: Mon Nov 29 2010 - 21:43:11 CST

Dear VMD users,


I am hoping someone can help me out with a modelling quandary I am
having (please forgive my ignorance of the issue, as I have just started
using 3D protein modelling programs).


I would like to generate a 3D model of a viral capsid (WUV) which has
not had any of it's structures determined by x-ray crystallography;
however, but a closely related virus (SV40) has. My question is; can I
use VMD to build a predicted WUV capsid based off of it's capsid AA
sequence, with the SV40 capsid .pdb file acting as a homology guide?


So far, I have used I-TASSER to generate several .pdb candidate
predictions of the WUV major capsid protein, but I am unsure of how to
proceed in mapping it onto that of the SV40 capsid .pdb file (1SVA). Oh,
and the capsid formation is fairly simple; the monomers form pentamers,
of which 72 join together to form the capsid.


Any help would be greatly appreciated!






Seweryn Bialasiewicz, PhD

Queensland Paediatric Infectious Diseases Laboratory,

Sir Albert Sakzewski Virus Research Centre

Building C28, Back Rd.

Herston, QLD 4029


t: +61.7.3636.8719

f: +61.7.3636.1401