PROCOMP

Protein comparison

• Compares residue-by-residue geometry of a set of closely-related protein structures.

Useful for closely related structures, such as:-

• Members of a family of proteins
• Models of a structure saved at different stages of refinement
• Homology model and structure on which it is based
• PostScript files produced:
  • Ramachandran plot for all residues in all structures
  • Ramachandran plot for Gly & Pro only
  • Chi1-chi2 plots
  • Dihedral angles, compared on a residue-by-residue basis:
    • Phi torsion angle
    • Psi torsion angle
    • Chi-1 torsion angle
    • Chi-2 torsion angle
    • Residue-by-residue Ramachandran plots
    • Residue-by-residue chi1-chi2 plots
  • Residue properties, including:
    • Absolte chi-1 deviations
    • Absolte omega torsion angle deviations
    • Average secondary structure
    • Circular variances of the dihedral angles
    • RMS deviations for main-chain and side-chain atoms
    • Residue-by-residue G-factors
  • Secondary structure in each model

Note. At present the program assumes that the residue-numbering between the PDB files corresponds to equivalent residues (though allowance is made for insertions and deletions). It also assumes that the structures have already been fitted and superposed on the equivalent residues.

Future versions will allow an alignment between the structures to be supplied so that equivalent residue-numbering will no longer be a requirement, and will also perform the fitting.

PROCOMP is available as part of PROCHECK.

Related programs:

• PROCHECK
• PROCHECK-NMR