InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology...

Area of Science:

• Computational biology
• Structural biology
• Bioinformatics

Background:

• Protein-protein interactions are crucial for cellular functions.
• Predicting these interactions computationally aids in functional characterization.
• Previous tools like InterEvDock utilized co-evolutionary information for docking.

Purpose of the Study:

• To introduce InterEvDock2, an advanced protein docking server.
• To expand functionality beyond structure-based inputs to include sequences and multimeric complexes.
• To incorporate user-defined constraints for more accurate docking predictions.

Main Methods:

• Developed InterEvDock2 with modules for template search and comparative modeling.
• Integrated sequence and multimeric input capabilities.
• Utilized rigid-body sampling, consensus scoring with physics-based and statistical potentials, including co-evolutionary information.

Main Results:

• Benchmarked on 812 complexes from the PPI4DOCK database.
• InterEvDock2 identified correct models in the top 10 predictions for 29% of cases.
• Predicted at least one correct interface residue in 91% of cases, outperforming individual scoring functions.

Conclusions:

• InterEvDock2 represents a significant advancement in protein docking methodology.
• The server provides enhanced accuracy and flexibility for predicting protein-protein interaction structures.
• It is a valuable resource for the experimental biology community.