This service computes the change in solvent-accessible surface area (ΔSASA) of each residue at the interface of Protein 1 and Protein 2, as well as an estimate of each residue contribution to the binding free energy.
If the chains of Protein 1 and Protein 2 are not both specified, the software will assume that each chain on the uploaded pdb file is an individual protein, and thus it will compute each chain against all the others.
Currently the software ignores everything that is not a polypeptide chain. That includes DNA/RNA chains, ions and organic molecules.
The calculation time may range from a few seconds to hours depending on the size of the proteins and on our server load. The results will be available online for 15 days.
We have pre-computed more than 30,000 PDB entries and stored the results on a database. If your file is an entry on the Protein Data Bank, the results may be readily available here.