MD Simulations Flashcards
1
Q
Why is molecular dynamics important?
A
Dynamical properties of proteins key elements in; Conformational enzyme changes Molecular motors Protein folding PPIs Allosteric protein regulation Membrane transport. Link between structure and dynamics!
2
Q
Give an example of how MD simulations have aided drug discovery efforts.
A
p53 - experimental structures have occluded a dynamic binding pocket.
This pocket on surface of p53 is a potential target to reactivate p53 cancer-related mutants.
3
Q
What is the use of MD force fields?
A
Provide equations and parameters to calculate potential energy of a protein from its atoms coordinates.
4
Q
what is explicit salvation model?
A
Water molecules explicitly included in simulated system.
Accurately describe specific solvent-solute interactions
But expensive as Nwat^2 calculations
5
Q
What does 0.01 TFlop/s mean?
A
Measure of computer speed = trillion floating point operations per second.
