Supercomputer Docking: Investigation of Low Energy Minima of Protein-Ligand Complexes

Danil C. Kutov; Alexey V. Sulimov; Vladimir B. Sulimov

doi:10.14529/jsfi180326

Authors

Danil C. Kutov Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation Dimonta Ltd., Moscow, Russian Federation
Alexey V. Sulimov Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation Dimonta Ltd., Moscow, Russian Federation
Vladimir B. Sulimov Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation Dimonta Ltd., Moscow, Russian Federation

DOI:

https://doi.org/10.14529/jsfi180326

Abstract

It is shown that the global energy minimum of a protein-ligand complex, when the energy is calculated by the PM7 quantum-chemical semiempirical method with the COSMO implicit solvent model, can be determined as follows. First, the low energy minima are found by a docking program when the protein-ligand energy is calculated with the MMFF94 force field in vacuum. Second, energies of all these minima are recalculated with the PM7 method and the COSMO implicit solvent model. Third, among these recalculated energies the minimal energy is determined and the respective minimum is the global energy minimum when the energy is calculated with the PM7 method and the COSMO implicit solvent model. The optimal width of the spectrum of low energy minima found with MMFF94 in vacuum is determined to perform minimal quantity of quantum-chemical recalculations. The proposed approach allows to perform docking in solvent with the quantum-chemical method and to increase the docking positioning accuracy.

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