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- W2900457624 endingPage "538" @default.
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- W2900457624 abstract "The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics-generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescored docking poses to phosphodiesterase 4B. Combined with stability and atomic distance analysis, MMGBSA helped to (c) identify the binding modes and sites of metabolism of cytochrome P450 2A6 substrates. The standard deviation of estimated binding energy within one simulation was lowered by minimization in all three example cases. Minimization improved the identification of the correct binding modes of androgen receptor ligands. Although only three case studies are shown, the results are analogous and indicate that these behaviors could be generalized. Such identified binding modes could be further used, for example, with free energy perturbation methods to understand binding energetics more accurately." @default.
- W2900457624 created "2018-11-29" @default.
- W2900457624 creator A5037452795 @default.
- W2900457624 creator A5056558644 @default.
- W2900457624 creator A5086418999 @default.
- W2900457624 creator A5090456130 @default.
- W2900457624 date "2018-12-23" @default.
- W2900457624 modified "2023-09-29" @default.
- W2900457624 title "Suitability of<scp>MMGBSA</scp>for the selection of correct ligand binding modes from docking results" @default.
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- W2900457624 doi "https://doi.org/10.1111/cbdd.13446" @default.
- W2900457624 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/30468569" @default.
- W2900457624 hasPublicationYear "2018" @default.
- W2900457624 type Work @default.