Introduction

Overview

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.

Applications

The SZMAP distribution comprises 2 applications:

SZMAP

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.

GamePlan

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.

Utility Programs

The following utility programs are also included in this distribution:

  • FixDupAtomNames: This program can be used during protein and ligand preparation to identify and rename any duplicate atom names which can confuse reduce, an open-source program used to add and optimize hydrogens.
  • MKHetDict: This program creates a PDB heterogen dictionary enabling reduce to add hydrogens to ligand atoms.
  • Pch: This program assists in preparing structure files for use with SZMAP by adding partial charges and radii to atoms and partitioning the molecules into separate protein and ligand files
  • 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.