Re: [ccp4bb] loop modelling?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: loop modelling?
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2009-11-01

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Subject: Re: loop modelling?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-11-01

Subject: Re: loop modelling?
From: Mensur Dlakic mdlakic {- at -} MONTANA {- dot -} EDU
Date: 2009-11-01

Hi Tommi,

I suggest Rapper ( http://mordred.bioc.cam.ac.uk/~rapper/ ). If you scroll
down to the bottom of the page, you'll find references both for ab initio
an map-based modelling. If you don't want to experiment with Rapper - it
may take some time to learn how to use it - send me a private message for a
script that will rebuild a loop in an existing PDB file. I use this script
to rebuild loops in comparative models that were built without the template.

MODELLER ( http://salilab.org/modeller/modeller.html ) also can do ab
initio loop modelling.

Hope this helps,

Mensur

At 05:29 AM 11/1/2009, Tommi Kajander wrote:
>Dear all
>I was wondering if anyone knows a simple way to generate a missing
>loop (strech of amino acids)
>really in just some simple manner (no fancy minization necessary, of
>course some constraints probably dont
>hurt), just for visualization purposes of further simulations etc....
>
>thanks!
>tommi

==========================================================================

Mensur Dlakic, PhD
Tel: (406) 994-6576

Department of Microbiology
Fax: (406) 994-4926

Montana State University
Lab: (406) 994-6237

109 Lewis Hall, P.O. Box 173520
http://myprofile.cos.com/mensur

Bozeman, MT 59717-3520
E-mail: mdlakic@montana.edu

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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: loop modelling?
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2009-11-01

Next message:
Subject: Re: loop modelling?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-11-01