Re: patch missing residues

From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Mar 17 2010 - 01:10:27 CDT

Bin,

1. BLAST the sequence to see if similar sequences with solved structures
exist.

2. Use one of the many Secondary Structure Prediction Servers freely
available:

http://bioinf4.cs.ucl.ac.uk:3000/psipred/
http://www.compbio.dundee.ac.uk/www-jpred/
http://bonsai.lif.icnet.uk/bmm/dsc/dsc_read_align.html
http://kestrel.ludwig.ucl.ac.uk/zpred.html
* * http://www.embl-heidelberg.de/predictprotein/
* * http://www.ibcp.fr/predict.html
* * http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html
http://bmerc-www.bu.edu/psa/
http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html

Chris

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Mon, Mar 15, 2010 at 3:42 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
> Dear all:
>
> I'm trying to work on a membrane protein, but the PDB file has some missing
> residues (~20). I can use MODELLER to add them and construct a complete
> structure. But since I have no idea what conformation these residues would
> adopt, I started with random loop. It seems to me the loop would take quite
> a long time to relax. So my question is: is there a more elegant way in this
> situation? Should I perform more intense minimization, perhaps simulated
> annealing, before any MD simulation? If you happen to have a good reference,
> that would be great.
>
> Thanks,
> Bin
>
>
>

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