Protein-Protein Docking Distance Restraints

If you know which parts of the protein should be in contact, you can add distance restraints between residues in the two proteins. These restraints define a minimum and a maximum distance between a residue in one protein (the receptor) and a residue in the other protein (the ligand). Individual restraints can be combined to satisfy some or all of a set of restraints. Restraint groups can be defined, and each group must be satisfied (there is a logical AND between groups). See Distance Restraints tab for more information on setting up distance restraints.

If, for example, you want to define restraints between two surface patches (such as from the Protein Surface Analyzer Panel), you can do so by defining groups. In this scenario, each residue in one patch must satisfy a constraint with one of the residues in the other patch. To set up the restraints, you define a group for each residue in one patch. This should be the smaller patch, as the maximum is four groups, and hence the patch must have no more than four residues. In each group you define restraints between one residue in the first patch and all residues in the other patch. You then select At least for Poses must satisfyand enter 1 for the minimum number, so that the residue from the first patch is restrained to only one of the residues in the second. As you added all the residues from the other patch, the effect is that it doesn't matter which residue in the second patch is restrained to the residue from the first patch.