Subject: summary: peptide conformational search

From: Eric Hu <yhu_2003<<at>>yahoo.com>
Date: Mon, 9 Aug 2004 14:18:40 -0700 (PDT)

Here are the two answers I got. Thank Dirk and Jeff
again.

A co-worker made his PhD-Thesis on conformational
analysis of (cyclic) 
peptids, but its in German:
http://diss.ub.uni-duesseldorf.de/ebib/diss/show?dissid=150

Regards, Dirk.

A 21 residue peptide would not be tractable to a
systematic search.  Monte Carlo and/or
high-temperature molecular dynamics are your best
bets.  To get started with some ideas, you may want to
take a look at the following: 

1.  Prabhu NV, Siddiqui SA, McMurray JS, Pettitt BM.
2001. Structural basis for the activity of pp60c-src
protein tyrosine kinase inhibitors. Biopolymers 59:
167 
2.  Levy Y, Becker OM. 2001. Energy landscapes of
conformationally constrained peptides. J. Chem. Phys.
114: 993 
3.  Worth GA, Nardi F, Wade RC. 1998. Use of multiple
molecular dynamics trajectories to study biomolecules
in solution: The YTGP peptide. J Phys Chem B 102: 6260

There are many other examples in the literature. 

Jeff 

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