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- W1988921808 abstract "The pH is an important parameter in macromolecular systems as it determines the protonation state of ionizable groups and consequently influences the structure, dynamics and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fix and cannot adapt to changes of the local environment. Here, we present a method to perform molecular dynamics simulations in explicit solvent at constant pH. During the simulation the protonation states of titratable groups are allowed to change dynamically, and the titration curves agree with experiment. Our method is based on the lambda-dynamics approach, in which the dynamics of the titration coordinate lambda is driven by generalized forces between the protonated and deprotonated states. Constant pH simulations can be achieved by accounting for the pH dependence of the hydration free energy. As a benchmark, titration curves of amino acid analogues and a di-peptide, as well as of turkey ovomucoid inhibitor protein were calculated." @default.
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- W1988921808 date "2011-02-01" @default.
- W1988921808 modified "2023-09-26" @default.
- W1988921808 title "In Silico Titration of Biomolecules: Explicit Solvent Constant pH Molecular Dynamics" @default.
- W1988921808 doi "https://doi.org/10.1016/j.bpj.2010.12.3529" @default.
- W1988921808 hasPublicationYear "2011" @default.
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