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,
or 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.
Either Choose a pdb-file,
Or Choose your own file

See our validation related articles for more background details regarding the validation servers. See also the WWW based validation explanation. 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, Gert Vriend.

Last modified Mon Jan 29 12:33:00 2018