Accurately Predicting Protein p <i>K</i> <sub>a</sub> Values Using Nonequilibrium Alchemy
Carter J. Wilson, Mikko Karttunen, Bert L. de Groot, Vytautas Gapsys
Abstract
values of coupled residues and observe a substantial performance disparity associated with the lysine partial charges in Amber14SB/Amber99SB*-ILDN, for which an underused fix already exists.
Topics & Concepts
ProtonationNon-equilibrium thermodynamicsChemistryThermodynamicsStatistical physicsLysinePhysicsComputational chemistryBiological systemAmino acidIonBiochemistryOrganic chemistryBiologyComputational Drug Discovery MethodsProtein Structure and DynamicsFree Radicals and Antioxidants