First off, thanks to all those who sent me their suggestions, a great
variety indeed. Here's the summary:
- turbo-frodo can do local rotamer optimization based on environment.
- SCRWL and WHAT-IF are servers for homology modeling
- Swiss PDB viewer/DeepView can also do homology modeling, but
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
[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
On May 13, 2011, at 4:00 PM, Tom J. Brett wrote:
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
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.
Thanks.
Andreas
--
Hi Andreas,
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.
PyMOL has a Mutagenesis wizard but
You can try Swiss-PDB viewer..
2011/5/12 Thomas Holder thomas.hol...@tuebingen.mpg.de
Hi Andreas,
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
Hi Andreas
Without the x-ray data, phenix.pdbtools might do this
(http://www.phenix-online.org/version_docs/dev-712/pdbtools.htm)
From the website:
[phenix.pdbtools can] Perform model geometry regularization. Minimize
geometry target to idealize bond lenghths, bond angles, planarities,
Or try SCWRL from Dunbrack's lab...
--- On Thu, 5/12/11, gauri misra kamga...@gmail.com wrote:
From: gauri misra kamga...@gmail.com
Subject: Re: [ccp4bb] mutation and minimization
To: CCP4BB@JISCMAIL.AC.UK
Date: Thursday, May 12, 2011, 12:52 PM
You can try Swiss-PDB viewer..
2011/5/12 Thomas
@JISCMAIL.AC.UK] On Behalf Of Andreas Förster
[docandr...@gmail.com]
Sent: Thursday, May 12, 2011 11:35 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] mutation and minimization
Hey all,
I would like to introduce point mutations in a structure and quickly
(and dirtily) minimize the new residue. (Best rotamer
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