On a similar extension to this topic, is there a good software out there for doing these kinds of modifications and minimizations for protein structures with chemicals entities (i.e., protein/inhibitor complexes). What I am looking to do is take a protein/inhbitor complex and add chemical modifications onto the inhibitor and see how they fit. so a little minimization/relaxation of the surrounding protein would be nice. It there a freely available software that will allow something like this, if not what commercial packages are cheapest/best at this? Thanks and sorry for hijacking this thread.
-tom
Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110
http://brettlab.dom.wustl.edu/
________________________________________
From: CCP4 bulletin board [[log in to unmask]] On Behalf Of Eric Pettersen [[log in to unmask]]
Sent: Friday, May 13, 2011 2:59 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] mutation and minimization
On May 12, 2011, at 4:00 PM, CCP4BB automatic digest system wrote:
Hey all,
I would like to introduce point mutations in a structure and quickly
(and dirtily) minimize the new residue. (Best rotamer dependent on
local environment, or the like.) What are simple approaches that don't
involve VMD/NAMD or some such overkill.
Chimera is pretty good for this. It has a Rotamer tool for making the substitution based on Dunbrack or Richardson libraries, and can screen based on probability / H-bonds formed / steric clashes:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/rotamers/rotamers.html
You can then use Chimera's Minimize Structure tool to minimize the side chain and/or the local environment or, if you're feeling frisky, the whole protein:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/minimize/minimize.html
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
Chimera home page: www.cgl.ucsf.edu/chimera<http://www.cgl.ucsf.edu/chimera>
|