SCCOMP

SCCOMP is a program for side chain modeling. It uses a scoring function that includes terms for complementarity (geometric and chemical compatability), excluded volume, internal energy based on probability of rotamers, and solvent accessible surface. The program has an accuracy of 92-94% for correct Chi1 prediction (± 40°) of buried residues, 82-84% for all residues, and about 1.7 Å for overall rmsd (not including Cβ). The exact values depend on the searching procedure. A fast iterative search, takes about a minute on the web server for a typical protein. A slower stochastic method takes about 12 minutes and improves the prediction by about 2% and 0.1 Å rmsd.
The program also permits:
1. Modeling only a subset of residues
2. Performing any number of mutations
3. Using an homologous structure as a template.

At this site you can download the source code for sccomp for different Unix/Linux platforms. You can also use our web server for modeling. The results are sent back by Email.
get sccomp source code
To use the web server follow the instructions below. You must fill one of the two first windows, either to submit your own coordinates or to specify a PDB id.
Every residue should include at least the backbone coordinates. The order of the atoms should follow that of the PDB format. The file should end with ".pdb" .

Enter your protein file.

Enter PDB id

Enter PDB chain (by default all chains will be modeled)

To model a residue (side chain only): specify position(s) (according to the PDB ATOM section) and residue type (3 letter code, case insensitive). If the residue type is not specified, the amino acid that appears at the input file at this position will be modeled.
To model the entire region in direct contact with the side chain (entire region): change selection in the mode window.

position chain (optional) residue type
mode

Output PDB file

Enter your Email. The PDB format model will be sent to this adress

Advanced options (optional)

Search type (by default, an iterative search will be performed)

Minimum probability (from rotamer library) for rotamer to be included in the search (by default, 0.003 is used)

In publications please refer to:

Eyal,E., Najmanovich,R., McConkey,B.J., Edelman,M. and Sobolev,V. (2004) Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. J. Comput. Chem., 25, 712-724.