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Benchmarking of different molecular docking methods for protein-peptide docking.

Piyush Agrawal^1,2, Harinder Singh², Hemant Kumar Srivastava²

¹Center for Computation Biology, Indraprastha Institute of Information Technology, Okhla Phase III, New Delhi, 110020, India.

BMC Bioinformatics

|February 6, 2019

Summary

This study benchmarks 6 molecular docking methods for protein-peptide interactions, finding FRODOCK excels in blind docking and ZDOCK in re-docking. A new web service, PPDbench, is introduced to aid researchers in calculating complex parameters.

Keywords:

ATTRACT Benchmark CAPRI FRODOCK Hex PatchDock Protein-peptide docking ZDOCK pepATTRACT

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Area of Science:

Computational Biology
Structural Bioinformatics
Molecular Modeling

Background:

Protein-peptide interactions are crucial but challenging to model due to peptide flexibility.
Existing docking method validation is limited for protein-peptide complexes.
This study addresses the need for rigorous benchmarking of peptide docking approaches.

Purpose of the Study:

To benchmark and evaluate the performance of six different molecular docking methods for protein-peptide complexes.
To assess docking accuracy using established criteria like FNAT, I-RMSD, and L-RMSD.
To identify the most effective docking strategies for modeling protein-peptide interactions.

Main Methods:

Benchmarking of 6 docking methods on 133 protein-peptide complexes (9-15 residues).
Evaluation using blind docking and re-docking strategies.
Performance assessment based on CAPRI parameters (FNAT, I-RMSD, L-RMSD).

Main Results:

FRODOCK showed superior performance in blind docking (avg. L-RMSD 3.72 Å).
ZDOCK achieved the best results in re-docking (avg. L-RMSD 2.88 Å for best pose).
AutoDock Vina performed well in re-docking on a smaller dataset (avg. L-RMSD 2.09 Å).

Conclusions:

FRODOCK is recommended for blind docking and ZDOCK for re-docking protein-peptide complexes.
Current pose ranking schemes require improvement for better accuracy.
A web-based service, PPDbench, was developed to assist the scientific community in analyzing docking results.