PatchDock

PatchDock predicts structures of protein-protein and protein-small molecule complexes by matching molecular surface shapes using geometric shape complementarity for molecular docking.

Key Features:

• Geometric shape complementarity: Identifies interacting partners by matching complementary molecular surface patches using geometric criteria.
• Local shape feature matching: Focuses on local surface features rather than exhaustive global sampling to detect compatible interfaces.
• Non-exhaustive 6-dimensional search: Avoids exhaustive searches in the full 6-dimensional transformation space to improve computational efficiency.
• Permitted steric clash: Allows some degree of steric clash at interfaces to retain near-native solutions that might be excluded by strict clash filtering.
• Ranking by shape complementarity: Produces a ranked list of potential complexes based on shape complementarity criteria.
• Scalability for large-scale docking: Employs the shape-based approach to enable efficient large-scale docking experiments.
• Flexible (hinge-bent) docking extension: Can be extended to accommodate hinge-bent flexible docking scenarios.
• Evaluation in CAPRI: Demonstrated performance in CAPRI rounds 1 and 2.
• Integration: Implemented as part of the BioInfo3D suite.
• Input formats: Accepts protein PDB codes and uploaded protein structures as input.

Scientific Applications:

• Protein–protein complex prediction: Predicts candidate docking orientations and interfaces for protein-protein interactions.
• Protein–small molecule docking: Identifies potential binding modes for protein-small molecule complexes using surface complementarity.
• Large-scale docking screening: Enables screening of many receptor-ligand pairs due to reduced computational search space.
• Method benchmarking and validation: Serves in benchmarking and validation efforts such as CAPRI participation.
• Structural biology studies: Assists in generation of structural hypotheses for experimental follow-up in structural biology research.

Methodology:

Matches molecular surface patches using geometric shape complementarity and local feature matching, avoids exhaustive searches in the 6-dimensional transformation space, permits limited steric clash at interfaces, and ranks resultant candidate complexes by shape complementarity; can be extended for hinge-bent flexible docking.