Simply conducting an MD simulation is an examination of "dynamic behavior," but unfortunately that term is far too vague to even have meaning. All biomolecules are dynamic. What is of interest is what makes them functional.
Simply conducting an MD simulation is an examination of "dynamic behavior," but unfortunately that term is far too vague to even have meaning. All biomolecules are dynamic. What is of interest is what makes them functional.
Exactly ("biomolecules are dynamic"). But the questioner asked about "analyses", here are some: normal mode analysis, essential dynamics, number of hydrogen bonds, radius of gyration, take your pick ...
Indeed there are numerous options. If the OP provides more detail about the system of interest and the relevant scientific question(s), then we can provide much better guidance. There are so many analyses that are simple to perform, but could end up being a waste of time depending on the real question(s) at hand.
I agree with previous posts that you first have to wonder why you ran the mentioned MD, then you'll find out what you want to get from it.
Typical analysis are RMS fluctuations (with respect to the average structure) or RMS deviation with respect to the initial structure.
Principal Component Analysis is also a useful technique to reduce the dimensionality of your results.
In this paper we did an alternative analysis that gave the dynamics at different time-scales:
http://pubs.acs.org/doi/abs/10.1021/ct200877z
Article Dynamic Fingerprints of Protein Thermostability Revealed by ...
Thank you for the opinion. Yes sure. Actually, I should explain the details of project in the previous question.
My question is actually on how to tell the people about the dynamics behavior of the protein in a smooth storyline.
For example :
1. Conformational stability, 2. dynamics behaviour of the conformation such as the flexibility, aggregation.
I am doing a protein-carbohyrate complexes to produce a new drug formulation. I am done with the analysis of the complexes conformational stability such as the RMSD, RMSF, and radius of gyration.
Previously, I was reading the article of 'essential dynamics of protein' by Amadei by could not understand it very well.
If you have any good links to be shared, just let me know. Thank you everyone!
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