PSSM

From Proteinfunction.net

PHUNCTIONER

 
Florencio Pazos et al [1] presented structure based function prediction by automatic identification of functional sites called PHUNTIONER. This method extracts 3D profiles of conserved residues for proteins with the same function. Primary intention of this method is for the case when there's no strong sequence similarity with proteins of known function.

Schematic diagram of PHUNCTIONER (Figure from Florencio Pazos et al, PNAS, 101,14754)

 

Reference

Automated prediction of protein function and detection of functional sites from structure, Florencio Pazos, and Michael J. E, Sternberg, PNAS, 101,14754