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J Chem Theory Comput. 2012 Sep 11;8(9):3395-408. doi: 10.1021/ct300497z. Epub 2012 Aug 14.

MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.

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Unidad de Bioinformática, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco UAM, E-28049 Madrid, Spain.
Departamento de Farmacología, Universidad de Alcalá, Alcalá de Henares, E-28871 Madrid, Spain.
SmartLigs Bioinformática S.L., Fundación Parque Científico de Madrid, c/Faraday, 7. Campus de Cantoblanco UAM, E-28049 Madrid, Spain.


An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.


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