Molecular Dynamics Simulation

Molecular dynamics (MD) simulation is a computer simulation technique that allows one to predict the time dependent evolution of a system of interacting particles using laws of physics. Studying the dynamic development of a biological system with the consideration of protein flexibility is of vital importance, since many biological phenomena involving proteins are very dynamic processes, which include transport, molecular recognition, enzyme catalysis, and allosteric regulation. The static models produced by NMR, X-ray crystallography, and homology modeling offer valuable insights into macromolecular structure, while MD simulation can provide atomic-level information about protein conformational changes and binding thermodynamics under predefined physiological conditions (e.g., temperature, pressure), allowing for the study of a protein system at a timescale that is not accessible by current experimental approaches.
Profacgen studies molecular dynamics of protein systems using state-of-the-art software tools.

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