Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

By Holger Gohlke, Christina Kiel, David A. Case. Journal of Molecular Biology, 2003

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EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization (2007, methodology): “39,40 We use a value of 0.0072 kcal/(mol A˚ 2 ) for the parameter r 41–43 and the SASA was calculated analytically in CHARMM.”
Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach (2020, methodology): “On the basis of the binding profiles, three FDA approved drugs (Remdesivir, Daraunvir and Saquinavir) and two compounds flavone and coumarin derivatives) from our in-house database were subjected to MD simulation studies and binding free energy calculation using the MM (GB/PB)SA method implemented i”