Coarse Packing Quality Control
Checks the normality of the local environment of amino acids
Checks the packing quality of proteins using the
method described in: Quality control of protein
models: Directional atomic contact analysis.
G. Vriend, C. Sander. J.Appl.Cryst. (1993) 26, 47-60.
This method is also called DACA for Directional
Atomic Contact Analysis. The idea is that the
distribution of atom types is determined around amino
fragments. We assume that the average distribution
observed in the PDB is representative for what can happen in
nature. Unlike many other methods, we do not
sperically average the distribution around the
fragment, but we keep the x,y,z directionality of
the contacts. The quality of any structure is now
easily determined by a convolution of the
average distributions and the observed contacts in
the protein to be checked.
If a residue has a score of -5.0 or lower, something
is really going on:
the residue makes symmetry contacts,
is contacting a ligand or an ion,
something is wrong.
See also chapter 11 of
the WHAT IF writeup.
This packing quality server is better for NMR
structures and low resolution
( > 2.0 Ångstrom) Xray structures.
The fine packing quality
control server is better for Xray structures.
See our validation related
for more background details regarding the validation
servers. See also the WWW based validation
If you have detected any error, or have any question or suggestion,
please send an Email to Gert Vriend.
Roland Krause, Maarten L Hekkelman, Jens E Nielsen,
Last modified Mon Jan 29 12:33:00 2018