Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI

Area of Science:

• Structural biology
• Computational biophysics
• Bioinformatics

Background:

• Accurate prediction of protein-protein and peptide-protein complexes is crucial for understanding biological processes.
• The CAPRI (Critical Assessment of PRedicted Interactions) experiment benchmarks protein-protein docking methods.

Purpose of the Study:

• To evaluate the performance of the ATTRACT coarse-grained docking approach combined with flexible refinement methods for predicting protein complexes.
• To assess the success rate and quality of predictions in CAPRI rounds 28-36.

Main Methods:

• Application of the ATTRACT coarse-grained docking approach.
• Integration with various atomistic, flexible refinement techniques.
• Utilizing template-based modeling and molecular dynamics-based refinement for specific cases.

Main Results:

• A 67% success rate (12 out of 18 targets) was achieved, generating at least one model of acceptable or better quality.
• Excellent predictions were obtained for several peptide-protein complexes.
• Medium to high-quality solutions were achieved by combining template-based modeling with molecular dynamics refinement.

Conclusions:

• The ATTRACT approach, coupled with flexible refinement, demonstrates significant success in predicting protein and peptide-protein complexes.
• New methods for interface refinement and ab-initio peptide-protein docking have been developed based on CAPRI experiences.
• Further improvements in scoring and handling protein flexibility are areas for future development.