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Published on Jul 8, 2008
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.