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• W2969740023 abstract "We provide a practical guide for using molecular dynamics simulation to compute the binding affinity of small molecules in complex with G-quadruplex DNA. Such calculations have a number of applications, such as rescoring docking results and validating docked poses, to inform the discovery of G-quadruplex binders with high affinity and selectivity. This chapter describes two binding free energy protocols: the double decoupling method (DDM) and the potential of mean force method (PMF). We illustrate the application of the two methods using a recent case study of the binding of quindoline with the c-MYC G-quadruplex DNA. For this system, the two methods yield absolute binding free energies within ~2 kcal/mol of the experimental value. We discuss the advantages and disadvantages of these binding free energy methods." @default.
• W2969740023 created "2019-08-29" @default.
• W2969740023 creator A5086612605 @default.
• W2969740023 date "2019-01-01" @default.
• W2969740023 modified "2023-10-17" @default.
• W2969740023 title "Using Molecular Dynamics Free Energy Simulation to Compute Binding Affinities of DNA G-Quadruplex Ligands" @default.
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• W2969740023 doi "https://doi.org/10.1007/978-1-4939-9666-7_10" @default.
• W2969740023 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/31444750" @default.
• W2969740023 hasPublicationYear "2019" @default.
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