The SZMAP product uses a semi-continuum solvation theory, to analyze and understand if presence of water in the binding site has a stabilizing or destabilizing effect on a protein-ligand complex.
The SZMAP distribution comprises 2 applications:
The SZMAP program is an application for analyzing sites on the surface of a protein and/or ligand using an explicit probe molecule, usually water, and producing 3D grids of estimated thermodynamic properties. SZMAP can also evaluate solvent thermodynamics rapidly at specified coordinates.The GamePlan tool identifies interesting coordinates near a ligand or in a protein binding site, runs SZMAP, and analyzes the results, comparing ligand properties to the binding site environment, generating a set of hypotheses for ligand modification and identifying sites where water either stabilizes or destabilizes the complex.
The following utility programs are also included in this distribution:
- Spruce4Szmap: This program can be used to prepare the protein structure, including building partial side-chains, capping chain breaks, placing and optimizing protons, assigning partial charges and radii.
- SzmapGrid: This program displays information about grids within an OE binary file (.oeb) and can split out a particular grid into a separate file. It also displays property tags in -at_coords results.
- GridComp: This program performs various mathematical operations on a grid or pair of grids to facilitate grid comparisons.
- SzmapReport: This program produces .pdf files containing 2D renderings of SZMAP results using the OEDepict and Grapheme technology.
A Word About Pronunciation¶
Like a number of OpenEye product names, SZMAP (solvent-zap-map) contains the letter pair sz which sounds similar to sh. It is pronounced ‘shmăp.