Recent development in computational science : Selected Papers from the International Symposium on Computational Science - International Symposium on Computational Science Kanazawa University, Japan
巻
4
ページ
71 - 78
発行年
2013-02-01
ISSN
2223-0785
出版者
Kanazawa e-Publishing
抄録
Accurate methods of computing the affinity of ligand with protein target are strongly needed in the drug discovery process. Many attempts have been made and several algorithms have been developed for this purpose. We compared the protein-ligand binding free energies (∆G) in various methods include docking score function, combining docking score function and molecular dynamics (MD) simulation with explicit and implicit solvent model, and molecular-mechanics Poisson Boltzmann surface area (MM-PBSA) approach with and without the inclusion of entropic contributions. We tested these various methods to human plasminogen kringle-3 domain protein with the ligand trans-(aminomethyl) cyclohexanecarboxylic acid (AMCHA). The results showed the comparison between these various methods and the experimental affinity value. We found that combining docking score function and MD simulation with explicit solvent model was more favorable and close to the experimental result. This indicated that combining docking score function and MD simulation with explicit solvent model could be more accurate and effective in the protein-ligand binding free energy calculation.
Binding Free Energy of Protein-Ligand by Combining Docking and MD Simulation: A Comparison of Calculation Methods
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