Transition Path of the Activation Loop in c-Src

A molecular dynamics simulation study of the activation of human c-Src tyrosine kinase using the string method with swarms-of-trajectories.

Using PDB 2SRC/1Y57 as two end-point structures, first we generate an initial activation pathway from targeted molecular dynamics simulation. The string is represented by connecting a series of discrete images extracted from the initial path. The local drift of each image along the string is estimated from a swarm of short trajectories and each image is updated correspondingly. After smoothing and re-parametrization of the string, a set of new images are generated. These steps are iterated until the string is well converged.

For more information about the methodology, see recent paper:
Finding transition pathways using the string method with swarms of trajectories. Pan AC, Sezer D, Roux B. J Phys Chem B. 112(11):3432-40, 2008.

Website: http://thallium.bsd.uchicago.edu/RouxLab/

Category:

Science & Technology

Tags:

• molecular
• dynamics
• simulations
• transition
• pathway
• string
• method
• Src
• kinase
• activation