Tuesday, August 28, 2012

Displaying disagreements in protein structures

I recently made a post on how to color a protein structure by disagreements between experimental chemical shifts and chemical shifts predicted from the structure.

Here is another way to display these kinds of errors, which I also find quite nice. Atoms radii are scaled proportionally the error in predicted chemical shifts.

Picture from http://dx.doi.org/10.1021/ct200913r (paywall)

In the above example, chemical shifts are determined from quantum chemical calculations on a 23 residue protein structure, and then compared to the corresponding experimental chemical shifts.
It's clear, that calculated chemical shifts from several side chains atom do not reproduce the experimental values as well as the backbone atoms chemical shifts. Definitely useful to identify possible errors in the protein structure

Frank et al. J. Chem. Theory Comput., 2012, 8 (4), pp 1480–1492

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