Hi Donnie,
On Mon, 04 May 2009 12:15:23 -0700, Donnie Berkholz
<[log in to unmask]> wrote:
> On 13:58 Mon 04 May , Robert Campbell wrote:
> Thanks, Rob!
>
> I've come across a web-based application called PepBuild that I'm using
> for the moment because I only need a few right now, so manual creation
> is fine. I'll give this a shot later on because I'm thinking about some
> more automated testing.
Come to think of it, there is also Tinker (http://dasher.wustl.edu/tinker/)
which has a program called "protein" whose description is:
PROTEIN
A program for automated building of peptide and protein structures. Upon
interactive input of an amino acid sequence with optional phi/psi/omega/chi
angles, D/L chirality, etc., the program builds internal and Cartesian
coordinates. Standard bond lengths and angles are assumed for the peptide.
The program will optionally convert the structure to a cyclic peptide, or add
either or both N- and C-terminal capping groups. Atom type numbers are
automatically assigned for the specified force field. The final coordinates
and a sequence file are produced as the output.
You can feed this an input file (it need not be interactive) and it will
very quickly generate coordinates. So if you are interested in building
many structures I think it would be the fastest way. The output is in Tinker
xyz format, but can be easily changed to pdb.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497
<[log in to unmask]> http://pldserver1.biochem.queensu.ca/~rlc
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