Re: [AMBER] Backbone

From: David A Case <>
Date: Wed, 18 Nov 2015 15:34:41 -0500

On Wed, Nov 18, 2015, mohammad r wrote:
> I mean that I have the sequence of a protein then I want the pdb file
> from that.

There is no general answer to this general problem (of going from sequence to
3D structure). In a practical sense, you will want to find out if a struture
for a similar sequence is available. If it is, then you almost certainly want
to look at comparative modeling (or "homology modeling"), and Amber is not
designed to do this.

For small, single-domain proteins, Amber simulations can be used to generate
"ab-initio" folds (not relying on having similar structures). See, e.g.

%A H. Nguyen
%A J. Maier
%A H. Huang
%A V. Perrone
%A C. Simmerling
%T Folding Simulations for Proteins with Diverse Topologies Are Accessible in
Days with a Physics-Based Force Field and Implicit Solvent
%J J. Am. Chem. Soc.
%V 136
%P 13959-13962
%D 2014

...good luck....dac

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Received on Wed Nov 18 2015 - 13:00:03 PST
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