New generation of docking programs: Supercomputer validation of force fields and quantum-chemical methods for docking
| Autor: | Vladimir B. Sulimov, I. S. Ilin, Danil C. Kutov, E. V. Katkova, A. V. Sulimov |
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| Rok vydání: | 2017 |
| Předmět: |
Models
Molecular Molecular model Binding energy 010402 general chemistry 01 natural sciences Force field (chemistry) Catalytic Domain 0103 physical sciences Materials Chemistry Computer Simulation Physical and Theoretical Chemistry Spectroscopy Simulation 010304 chemical physics Chemistry Proteins Computer Graphics and Computer-Aided Design Small molecule 0104 chemical sciences Molecular Docking Simulation Maxima and minima Protein–ligand docking Docking (molecular) Searching the conformational space for docking Quantum Theory Thermodynamics Biological system Protein Binding |
| Zdroj: | Journal of Molecular Graphics and Modelling. 78:139-147 |
| ISSN: | 1093-3263 |
| DOI: | 10.1016/j.jmgm.2017.10.007 |
| Popis: | Discovery of new inhibitors of the protein associated with a given disease is the initial and most important stage of the whole process of the rational development of new pharmaceutical substances. New inhibitors block the active site of the target protein and the disease is cured. Computer-aided molecular modeling can considerably increase effectiveness of new inhibitors development. Reliable predictions of the target protein inhibition by a small molecule, ligand, is defined by the accuracy of docking programs. Such programs position a ligand in the target protein and estimate the protein-ligand binding energy. Positioning accuracy of modern docking programs is satisfactory. However, the accuracy of binding energy calculations is too low to predict good inhibitors. For effective application of docking programs to new inhibitors development the accuracy of binding energy calculations should be higher than 1kcal/mol. Reasons of limited accuracy of modern docking programs are discussed. One of the most important aspects limiting this accuracy is imperfection of protein-ligand energy calculations. Results of supercomputer validation of several force fields and quantum-chemical methods for docking are presented. The validation was performed by quasi-docking as follows. First, the low energy minima spectra of 16 protein-ligand complexes were found by exhaustive minima search in the MMFF94 force field. Second, energies of the lowest 8192 minima are recalculated with CHARMM force field and PM6-D3H4X and PM7 quantum-chemical methods for each complex. The analysis of minima energies reveals the docking positioning accuracies of the PM7 and PM6-D3H4X quantum-chemical methods and the CHARMM force field are close to one another and they are better than the positioning accuracy of the MMFF94 force field. |
| Databáze: | OpenAIRE |
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