Restraints Tutorial
If you have knowledge about residues that should be close together in the interface, you can make a restraints file and use the knowledge you have to only produce results which satisfy your restraints. For example, NMR and cross-linking experimental data can provide information about interacting residues. Each restraint specifies a pair of residues, one each from the receptor and ligand, and an acceptable distance range for the restraint to be satisfied. Restraints can combined into restraint groups, and groups are combined into a restraint set, which allows users to specify some logic about how many restraints are required to be satisfied.
Restraints can either be in an AIR format, or in our JSON format. You can
download a sample AIR type restraint file here.
You can download the same restraints in our JSON format here.
The PDB ID 1F3G should be used as the receptor, and 1POH should be used
as the ligand.
We have also created a tool for generating restraints in our JSON format, which can be found here.
If you have any questions, please look to see if it is addressed on the help page. If you have any suggestions, please contact us.
Vajda Lab and ABC Group
Boston University and Stony Brook University