Molecule analysis made easy. The program Probe allows one to evaluate atomic packing, either within or between molecules. It generates "contact dots" where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file. Alternatively, the packing information can be quantified and displayed in a table listing scores for van der Waals interactions, H-bonds and atomic overlaps ("clashes"). Essentially the inverse of the Connolly algorithm, the approach is to place a very small probe (typically of radius 0.25A) at points along the van der Waals surface of a selected set of atoms and determine if this probe also contacts atoms within a second "target" set. Probe provides a flexible method for selecting the source and target atoms along with command line flags for altering the probe radius and dot density.

The license of this software is Freeware, you can free download and free use this calculator software.