Thursday, March 23, 2017

Equilibrium simulations: how can contact maps help?

In equilibrium, the animation of the contact maps can still be interesting, if for no other reason than to see that nothing much is happening (this is a 50 ns simulation of ubiquitin):

Again, we can check if we have gained or lost any contacts along the way:

Not much there! "encounter" is defined (in this case) as beginning if two residues are within 6 ångström of each other (defined as any two heavy atoms) and ending if two residues are farther than 7.5 ångström. This two-cutoff scheme avoids the detection of spurious encounters (say, if a distance keeps oscillating between 0.59-0.61, a single cutoff would yield many encounters while this one just one).

ConAn can also observe the average encounter time as well as number of encounters, although you should make sure that what you observe is actually a physical interaction.

However, this can be a quick "sanity check" or an initial screening. Furthermore, these measures can be very useful for unstructured proteins. In those cases, the above plots would be much more colorful! (Example analyses on IDP's are coming soon.)

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