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From Maximilian Scheurer, Peter Rodenkirch, Marc Siggel, Rafael C. Bernardi, Klaus Schulten, Emad Tajkhorshid and Till Rudack Biophysical Journal, Volume 114, Issue 3, 577-583:

One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability.

What are noncovalent interaction networks? And why their time evolution is important in structural biology. I tried also to use the authors' library pycontact, but it's not clear to me how to use it.

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  • $\begingroup$ @Mithoron, sigh fancy name for nothing new. I don't get what is so special about this approach. Applying a threshold to a pidst 2D matrix, ins't it trivial thing to do? $\endgroup$
    – 0x90
    Mar 19 '18 at 21:56
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    $\begingroup$ @Mithoron why the downvotes? Is the question not legitimate? $\endgroup$ Mar 19 '18 at 22:13
  • $\begingroup$ @ToddMinehardt, as opposed to grilled cheese an "interaction" based on contact map is a bit arbitrary selection. For example 2 amino acids are 0.2nm apart do they interact what if they are 0.21nm what if the threshold is 0.3nm and they are 0.30002nm apart have they stopped to contact? $\endgroup$
    – 0x90
    Mar 20 '18 at 12:57
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    $\begingroup$ This is not homework; please don't flag it as such. $\endgroup$ Mar 20 '18 at 13:31

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