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MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.
Javier Klett1, Alfonso Núñez-Salgado1, Helena G Dos Santos1
1Unidad de Bioinformática, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco UAM, E-28049 Madrid, Spain.
Journal of Chemical Theory and Computation
|November 26, 2015
Summary
A new scoring function, MM-ISMSA, accurately and rapidly predicts protein-protein docking. It combines molecular mechanics, implicit solvent models, and surface area calculations for efficient and reliable protein complex analysis.
Area of Science:
- Computational Biology
- Structural Biology
- Biophysics
Background:
- Protein-protein interactions are crucial for biological processes.
- Accurate prediction of protein complex structures is essential for understanding function.
- Existing scoring functions for protein docking can be computationally intensive.
Purpose of the Study:
- To develop an ultrafast and accurate scoring function for protein-protein docking.
- To assess the performance and accuracy of the new scoring function against established methods.
- To provide a tool for analyzing protein-protein complex formation and molecular dynamics trajectories.
Main Methods:
- Developed the MM-ISMSA scoring function, integrating molecular mechanics (12-6 Lennard-Jones), implicit solvent model with desolvation penalties and hydrogen bonding, and surface area contributions.
- Validated MM-ISMSA by comparing binding energies with APBSA and MM-PB(GB)SA on 1242 decoy complexes.
- Tested MM-ISMSA's ability to identify the near-native structure in 15 protein-protein complexes with decoys.
Main Results:
- MM-ISMSA demonstrated remarkable correlation (r(2) ~ 0.9) with established methods for binding energy calculations.
- Achieved high accuracy in identifying the correct docking pose, succeeding in 80% of test cases.
- Calculations are highly efficient, taking only 0.2-5.0 seconds per complex, including energy decomposition.
Conclusions:
- MM-ISMSA offers a significant advancement in speed and accuracy for protein-protein docking.
- The scoring function is robust and reliable for predicting protein complex structures.
- MM-ISMSA is available as a PyMOL plugin and in command-line mode for broad accessibility.
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