RPScore(Residue Level Pair Potential Scoring)
The RPSscore program uses an empirical pair potential matrix to score each possible complex. The pair potentials are at an amino acid residue level. Each potential corresponds to the empirically derived likelihood of a trans-interface pair of two residue types, limited only by a distance cut off (Moont et.al. 1999). The present most useful matrix used is generated from 103 non-homologous interfaces found in the PDB with the aid of SCOP 1.50 (http://scop.mrc-lmb.cam.ac.uk/scop/).
For a fuller description of the algorithm, installation instructions, a step by step tutorial, and program manual, please see the 3D-Dock Manual (PDF).