Protein-protein docking: is the glass half-full or half-empty?

Area of Science:

• Computational biology
• Structural biology
• Bioinformatics

Background:

• Assessing the capability of current protein docking methods to construct complexes from individual protein structures.
• Evaluating the impact of protein complex classification based on docking difficulty.

Purpose of the Study:

• To determine key properties for successful protein docking.
• To classify protein complexes by docking difficulty.
• To identify limitations of current docking methods.

Main Methods:

• Analysis of recent computational studies, including Critical Assessment of Protein Interactions (CAPRI) competition results.
• Classification of protein complexes based on docking difficulty.

Main Results:

• Enzyme-inhibitor complexes can be docked with reasonable accuracy.
• Antigen-antibody and small signaling complexes show less predictable docking results.
• Transient complexes with large interfaces are beyond the scope of current docking methods.

Conclusions:

• Current docking methods show varying success rates depending on protein complex type.
• Moderate experimental data can improve docking accuracy.
• Novel approaches are needed for docking transient complexes with large interfaces.