you should do some reading about homology modeling- what you suggest is an
active research area. Look at the programs people used for previous CASP
competitions, and read their work carefully. MD simulations could be used as
a final step for refinement, but you need to learn about programs for
homology (or "comparative") modeling.
2010/3/4 Shaandar Nyamtulga <nyam100.hotmail.com>
>
>
> I apologise for my vague question. I am planning to attend in CASP, even
> though I am novice to protein structure prediction. In which part of protein
> structure prediction I can use Amber? Within the limit of my knowledge, I am
> planning to compare the target protein sequence wth others using blast, and
> find some proteins which have similar parts (domains, motifs,..I guess),
> copy and paste those similar parts's structures and combine and edit
> (restructure) them in Pymol. I would really appreciate if someone would give
> me detailed guidance.
>
> Thank you
>
>
>
> Nyamtulga Shaandar, M.Sc
>
> Researcher,
>
> Informatics Institute,
>
> Mongolian Science Academy,
>
> Mongolia
>
>
>
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Received on Thu Mar 04 2010 - 04:30:04 PST
