The most important processes in a cell are regulated by proteins essentially, by interacting with other proteins or other molecules. Protein dynamic plays an important part in various disciplines like biology, chemistry, synthesis, computational modeling. It includes processes from fast movements that may cause protein collapse due to high friction, but such challenges can be tackled with molecular simulations and dynamics..
As per the history, the first molecular dynamics simulation (1950’s) was performed to study the interactions of hard spheres, followed by various dynamic simulations including the one on a realistic system. The first simulation on protein (bovine pancreatic trypsin inhibitor) was done in 1977 and then the advancements are never ending.
Molecular dynamics open up the information on fluctuations, conformational changes of proteins (folding) and Nucleic Acid, thermodynamics of biological molecules and complexes along with examination of structural stability of proteins’, DNA, complexes.Many simulation studies have been done on Protein-protein and protein-ligand interactions and interaction study of protein-protein is more complex than protein-ligand because of the size and relative potential interaction sites. For instance, in fragment based drug discovery where small molecules are used, molecular dynamic simulations are employed to study the binding pattern(s) and their related kinetics and energetics.
For good analysis, algorithm with efficient computational power, energy and momentum conservation, long time step is required. Therefore, we should be cautious in choosing algorithm as these complex expressions makes it very expensive.
http://pubs.acs.org/doi/pdf/10.1021/ci4006063
https://www.acellera.com/complete-protein-protein-kinetics-by-molecular-dynamics/
References
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