VMD-L Mailing List

From: Seweryn Bialasiewicz (seweryn_at_uq.edu.au)
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!

 

Cheers,

-Seweryn

 

 

Seweryn Bialasiewicz, PhD

Queensland Paediatric Infectious Diseases Laboratory,

Sir Albert Sakzewski Virus Research Centre

Building C28, Back Rd.

Herston, QLD 4029

Australia

t: +61.7.3636.8719

f: +61.7.3636.1401

e: seweryn_at_uq.edu.au