"function from structure"
Surface electrostatics, as displayed, (e.g., GRASP, Nicholls, et al.)
can identify DNA & RNA binding sites, occasionally, other features.
Thornton et al: small ligand binding sites are almost always associated with the largest depressions in the surface of a protein... visually
Conserved motifs in a family (on the surface of a structure) as a method of finding functional features, particularly protein-protein interaction sites.
3D catalytic motifs can be catalogued & used to identify the catalytic function of new structures.
Methods developed in drug design to identify potential lead compounds are expected to be applicable to deducing ligand-binding specificity.
http://www.nih.gov/nigms/news/meetings/structural_genomics_targets.html
http://bioinfo.mbb.yale.edu/genome/foldfunc/