CABS-dock

CABS-dock performs flexible protein–peptide docking to predict peptide binding sites and binding poses while accounting for substantial conformational flexibility of both peptides and proteins.

Key Features:

• Conformational Flexibility: Accommodates significant conformational changes in both peptides and proteins during the binding site search.
• Binding Site and Pose Prediction: Predicts peptide binding sites and binding poses on protein targets.
• Computational Approach: Implements in silico docking that integrates conformational sampling with docking simulations.

Scientific Applications:

• Peptide–protein interaction mapping: Prediction and mapping of peptide binding sites and poses to support analysis of molecular recognition and therapeutic design.
• Identification of peptide binders to PkMSP-1_19: Applied to peptides discovered by random linear dodecapeptide Ph.D.-12 phage display with three rounds of biopanning against the 19-kDa fragment of Merozoite Surface Protein-1 (PkMSP-1_19), where CABS-dock predicted binding sites confirming binders Pkd1 (HFPFHHHKLRAH) and Pkd2 (HPMHMLHKRQHG).

Methodology:

CABS-dock uses an in silico approach that integrates conformational sampling with docking simulations and allows substantial conformational flexibility of peptides and proteins during the binding site search.