Scalable Indirect Free Energy Method Applied to Divalent Cation-Metalloprotein Binding.

ABSTRACT: Many biological processes are based on molecular recognition between highly charged molecules such as nucleic acids, inorganic ions, charged amino acids, etc. For such cases, it has been demonstrated that molecular simulations with fixed partial charges often fail to achieve experimental accuracy. Although incorporation of more advanced electrostatic models (such as multipoles, mutual polarization, etc.) can significantly improve simulation accuracy, it increases computational expense by a factor of 5-20×. Indirect free energy (IFE) methods can mitigate this cost by modeling intermediate states at fixed-charge resolution. For example, an efficient "reference" model such as a pairwise Amber, CHARMM, or OPLS-AA force field can be used to derive an initial estimate, followed by thermodynamic

SUBMITTER: Litman J 

PROVIDER: S-EPMC11500062 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature