Bind3P: A Water Model to Improve the Accuracy of Binding Calculations

02 February 2018, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

We report a water model, Bind3P (Version 0.1), which was obtained by using sensitivity analysis to readjust the Lennard-Jones parameters of the TIP3P model against experimental binding free energies for six host-guest systems, along with pure liquid properties. Tests of Bind3P against >100 experimental binding free energies and enthalpies for host-guest systems distinct from the training set show a consistent drop in the mean signed error, relative to matched calculations with TIP3P. Importantly, Bind3P preserves the accuracy of bulk water properties, such as density and heat of vaporization. The same approach can be applied to more sophisticated water models that can better represent pure water properties. These results lend further support to concept of integrating host-guest binding data into force field parameterization.

Keywords

Drug design
binding free energy
binding enthalpy
host–guest
force field
water model
molecular dynamics
TIP3P
sensitivity analysis
attach-pull-release

Supplementary materials

Title
Description
Actions
Title
Bind3P-SI
Description
Actions
Title
Bind3P-uncertainties
Description
Actions

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