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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