scap is a program for protein side-chain prediction and residue mutation. It can make predictions on all residues or a certain number of residues in a protein of multiple chains. It automatically detects if the residue to be predicted or mutated is backbone only, or complete with all side-chain atoms. If the residue is backbone only, it will first add side-chains and then do predictions; if the residue is to be mutated, the residue is first mutated accordingly and prediction is then performed.
The current version of scap supports the following platforms: SGI 6.5, Intel Linux and Sun solaris.
Side-chain rotamer library
Dihedral rotamer library:
- Dihedral Rotamer library based on 135 proteins
- Dihedral Rotamer library based on 297 proteins
- Dihedral Rotamer library based on 533 proteins
- Dihedral Rotamer library based on 844 proteins
Coordinate rotamer library
All the rotamer library has the name such as: rotamer92_20_ang which has the following meaning:
- the first number 92 means the rotamer represent 92% sidechain conformations in all the protein datasets used to create the rotamer
- the second number 20 means the rotamer library is based on 20 degree torsional angle cutoff.
- the protein list is taken from Dunbrack sidechain homepage 98 version.
Xiang Z, Honig B. Extending the accuracy limits of prediction for side chain conformations. J Mol Biol. 2001 Aug 10;311(2):421-30.
Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side chain conformations. J Mol Biol. 2002 Jul 12;320(3):597-608.
scap is supported by a funding from the National Science Foundation Grant # DBI-9904841.
Developed in the Honig Lab.