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 [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eric Pettersen [p...@cgl.ucsf.edu] Sent: Friday, May 13, 2011 2:59 PM To: CCP4BB@JISCMAIL.AC.UK 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>
