New ProtoMol Project 10005

[jcoffland]

Project 10005 using the new ProtoMol core has just entered advanced methods.

ProtoMol uses methods for accelerated long-time dynamics of proteins, called Normal Mode Langevin (NML). Using NML allows for speedups of hundreds over plain molecular dynamics. The method repeatedly finds the low frequency directions using normal mode analysis, and projects the motion of the molecule along them while resolving the nearly instantaneous motion (see Sweet et. al., J. Chem. Phys., 2008, Vol 128, pp. 145101 and preprint at http://www.nd.edu/~izaguirr/papers/izaguirre-r1.pdf for more details). The goals of this project are threefold: to validate NML by simulating the folding and dynamics of the Fip35 WW domain, to understand the role of mutations on folding, and to understand the activation of src Kinase, an enzyme that is involved in the onset of some kinds of cancer.