Subject: CCL:protein side-chain

From: Antoine Logean <[email-masked]>
Date: Wed, 18 Sep 2002 19:28:51 +0200

Dear Xavier,

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 attempting to determine the distribution of side 
chain dihedral values of a subset of the PDB permitted to define mainly 
two different kind of 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.

other references :

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