Does anyone know if the pair term has changed since it’s introduction? Does it use the same pdb statistics and bins as described in:
Simons, K. T., Ruczinski, I., Kooperberg, C., Fox, B. A., Bystroff, C. & Baker,D. (1999) Proteins Struct. Funct. Genet. 34, 82–95.
It seems as though the term is the same for centroid and full-atom scoring. Is this true?
“The pair term is implemented somewhat differently in centroid and fullatom modes.
In centroid mode, distances are calculated between sidechain centroids.
In fullatom mode, distances are calculated between specific atoms, “action centers”, for each residue (e.g. ARG – the terminal carbon atom).
Fullatom pair term sidechain atoms are defined in the residue’s *.params file in:
chemical/residue_type_sets/fa_standard/residue_types/*/*.params
at the line labeled:
ACT_COORD_ATOMS
I’m not sure if/when the statistics were (re)-gathered.
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