cPEPmatch is a computational tool created to assist in the rational design of cyclic peptide mimetics capable of potentially
modulating interactions within protein-protein or protein-ligand complexes.
Step 1: Upload your target protein-protein or protein-ligand complex's crystal structure in PDB format
Step 2: Identify the protein chains you want to mimic and target in the uploaded PDB file. Make sure to specify the protein chain names exactly as they appear in the PDB file.
Step 3: Choose Parameters
Cutoff: Set the interface cutoff distance (Default: 6 Å).
Threshold: Choose the fit-RMSD maximum for a match (Default: 0.7 Å - Recommended: 0.5-1.0).
Motif Size: Define the motif length (Default: 5 amino acids, Recommended: Adjust based on binding site characteristics, 4-7).
(Optional) Residue Numbers: Specify specific residues if you know the binding hot spots. Hot spots are residues contributing the most
to binding free energy. Ensure that the number of residues specified is at least equal to the size of the motif.
Additionally, when this option is used, the recommended threshold for fit-RMSD is adjusted to 1-2 Å.
Step 4: Submit and Review: After submitting your job, you'll receive an email with a link to download a zip file containing your results. Review the results to identify potential cyclic peptide matches.
Enjoy the peptide design process and good luck with your research!
Or, for a more comprehensive guide with a practical example, check out our full tutorial.
