Gap regions between molecules

SURFNET locates gap regions between molecules by fitting spheres between all pairs of atoms, as described here.

A surface is then generated around the spheres to show the size and shape of the gap regions.

Examples

The following examples show the gap regions between the aspartic protease endothiapepsin and the inhibitor H-189 from PDB code 3er5, as visualized by three different programs:

Defining protein binding sites

The gap regions can also be computed for a single molecule - such as a protein. This gives all the molecule's internal cavities and surface grooves. It is possible to extract the relevant gap region from all the rest and so get the cavity or groove that corresponds to the protein's binding site.

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