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SUMMARY:Constrained Geometric Simulation of Diffusive Motion in Proteins -
  William Belfield (TCM)
DTSTART:20090206T160000Z
DTEND:20090206T163000Z
UID:TALK16256@talks.cam.ac.uk
CONTACT:Daniel Cole
DESCRIPTION:"Stephen Wells et al. Phys. Biol. 2 S127-S136 (2005)":http://d
 x.doi.org/10.1088/1478-3975/2/4/S07\n\nWe describe a new computational met
 hod\, FRODA (framework rigidity optimized dynamic algorithm)\, for explori
 ng the internal mobility of proteins. The rigid regions in the protein are
  first determined\, and then replaced by ghost templates which are used to
  guide the movements of the atoms in the protein. Using random moves\, the
  available conformational phase space of a 100 residue protein can be well
  explored in approximately 10–100 min of computer time using a single pr
 ocessor. All of the covalent\, hydrophobic and hydrogen bond constraints a
 re maintained\, and van der Waals overlaps are avoided\, throughout the si
 mulation. We illustrate the results of a FRODA simulation on barnase\, and
  show that good agreement is obtained with nuclear magnetic resonance expe
 riments. We additionally show how FRODA can be used to find a pathway from
  one conformation to another. This directed dynamics is illustrated with t
 he protein dihydrofolate reductase.
LOCATION:TCM Seminar Room\, Cavendish Laboratory
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