SZMAP
Water…where it matters, when it matters
SZMAP is an application to help modelers and medicinal chemists understand the role of water in molecular interactions such as ligand binding. It uses a single explicit probe water in a high-dielectric continuum solvent to rapidly map the magnitude and distribution of solvent energies near a molecular surface. This is referred to as a semi-continuum model [1, 2] and attempts to overcome potential limitations in continuum methods, such as our Poisson-Boltzmann (PB) approach in ZAP [3]. The method essentially involves building up thermodynamic quantities at points of interest by calculating energies of a thorough sampling of orientations of a discrete water.
Features
- Produces 3D grids mapping various thermodynamic quantities across holo, apo and ligand structures
- Performs very rapid calculations at specified sets of coordinates such as atom centers of bound ligands
- Includes a facility for integrating grids to quantify SZMAP results
- Prediction of changes in water activity on ligand binding
- Output of key waters and orientational preferences
- Variable resolution
- Results can be visualized in 3D using VIDA
- 2D Grapheme representations present SZMAP results in a format that is natural for a chemist
- Includes tools to convert output grids to different formats and perform various mathematical operations on grids
[1] Tanger, J.C., Pitzer, K.S., J. Phys. Chem. 1989, 93, 4941-4951.
[2] Rashin, A.A., Bukatin, M.A., J. Phys. Chem. 1991, 95, 2942-2944.
[3] Grant, J.A., Pickup, B., Nicholls, A., J. Comp. Chem. 2001, 22, 608-640.
