Subject: Re: CCL:protein side-chains

From: Antoine Logean <[email-masked]>
Date: Wed, 18 Sep 2002 10:26:20 +0200

Hi,

Side-chain modeling consists mainly in the right choice of dihedral
angles, Xi i = 1,2,3 and 4. Bond lengths and bond angles stay (more or 
less) constant and can be taken from force field parameters.

Statistical studies establishing distribution of dihedral values in a 
subset of the PDB give rise to different rotamer libraries :

Backbone dependent-rotamer library :

Dunbrack, R.L., Jr. and M. Karplus, Backbone-dependent rotamer library 
for proteins. Application to side-chain prediction. J Mol Biol, 1993. 
230(2): p. 543-74.

and his web site : http://www.fccc.edu/research/labs/dunbrack/bbdep.html

Backbone-independent rotamer library :

Lovell, S.C., et al., The penultimate rotamer library. Proteins, 2000.
40(3): p. 389-408.

and :

Summers, N.L. and M. Karplus, Construction of side-chains in homology 
modelling. Application to the C-terminal lobe of rhizopuspepsin. J Mol 
Biol, 1989. 210(4): p. 785-811.

Summers, N.L. and M. Karplus, Modeling of globular proteins. A 
distance-based data search procedure for the construction of 
insertion/deletion regions and Pro----non-Pro mutations. J Mol Biol, 
1990. 216(4): p. 991-1016.

McGregor, M.J., S.A. Islam, and M.J. Sternberg, Analysis of the 
relationship between side-chain conformation and secondary structure in 
globular proteins. J Mol Biol, 1987. 198(2): p. 295-310.

Bower, M.J., F.E. Cohen, and R.L. Dunbrack, Jr., Prediction of protein 
side-chain rotamers from a backbone-dependent rotamer library: a new 
homology modeling tool. J Mol Biol, 1997. 267(5): p. 1268-82.

good work

Antoine