Title: Solvation Structure and Thermodynamic Mapping (SSTMap): an open-source software package for the analysis of water in molecular dynamics trajectories. Understanding the underlying physics of ligand-protein molecular recognition is a key objective of computational chemistry and biology. The displacement and reorganization of water molecules from the active site upon the binding of a ligand is a principal, and often dominant, source of binding free energy however it is often treated simplistically in computational methods aimed at discovering new drug candidates or optimizing lead compounds/ In order to address this shortcoming, we, together with the Gilson group, have developed SSTMap, an open-source and freely distributed software package for mapping out structural and thermodynamic water properties in molecular dynamics trajectories. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory which is implemented in both hydration site-based (HSA) and grid-based (GIST) approaches. The package also maps out measures of local water network frustration and enhancement. We will discuss the capabilities of SSTMap and its potential applications in virtual screening and rational lead optimization.

Solvation structure and thermodynamic mapping (SSTMap): Open-source software package for the analysis of water in molecular dynamics trajectories

2019 Fall National Meeting

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