Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations

Journal of Chemical Theory and Computation
Bing XieDavid D L Minh

Abstract

We demonstrate the feasibility of estimating protein-ligand binding free energies using multiple rigid receptor configurations. On the basis of T4 lysozyme snapshots extracted from six alchemical binding free energy calculations with a flexible receptor, binding free energies were estimated for a total of 141 ligands. For 24 ligands, the calculations reproduced flexible-receptor estimates with a correlation coefficient of 0.90 and a root-mean-square error of 1.59 kcal/mol. The accuracy of calculations based on Poisson-Boltzmann/surface area implicit solvent was comparable to that of previously reported free energy calculations.

References

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Dec 11, 2019·Journal of Computational Chemistry·William M MenzerDavid D L Minh
May 19, 2020·Physical Chemistry Chemical Physics : PCCP·Soohaeng Yoo WillowDavid D L Minh
Dec 23, 2017·Journal of Computational Chemistry·Trung Hai NguyenDavid D L Minh
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Related Concepts

Molecular Dynamics
Muscle Rigidity
Ligand Binding
Lysozyme Test
Plasma Protein Binding Capacity
Lysozyme
Muramidase
Protein Conformation
Binding (Molecular Function)
Entropy

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