scap

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.

Download software

Click here to download scap.

System requirements

The current version of scap supports the following platforms: SGI 6.5, Intel Linux and Sun solaris.

Documentation

• Manual in pdf format

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

• coordinate Rotamer library based on 135 proteins
• coordinate Rotamer library based on 297 proteins

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.

References

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.

Acknowledgments

scap is supported by a funding from the National Science Foundation Grant # DBI-9904841.

Developed in the Honig Lab.