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SUMMARY:Understanding the Action of Proteins - Prof. Peter Bolhuis\, Unive
 rsity of Amsterdam (CCP5 Lecturer)
DTSTART:20120315T141500Z
DTEND:20120315T151500Z
UID:TALK35027@talks.cam.ac.uk
CONTACT:Robert Best
DESCRIPTION:Molecular dynamics simulation can in principle provide useful 
 predictions of processes involving protein conformational changes on an at
 omistic level that are complementary to experiment. However\, in practice\
 , all atom molecular dynamics is often limited to small systems due to the
  long simulation times required for such processes to take place. It is po
 ssible to bridge these long time scales by realizing that many processes s
 uch as (un)folding and other conformational changes in proteins in fact ar
 e rare events caused by (high) free energy barriers between stable states.
  To overcome such barriers\, many techniques have been developed\, e.g. re
 plica exchange\, metadynamics\, and transition path sampling. While proper
  sampling is important\, only proper analysis of the simulation results ca
 n yield insight. Proteins can adopt many configurations\, and it is not al
 ways easy to identify stable or metastable states and transitions between 
 them. The development of methods that describe protein dynamics in terms o
 f equilibrium kinetic networks or Markov state models have made such analy
 sis possible.  In addition\, we have recently developed methods that allow
  the prediction of relevant reaction coordinates.\n\nIn this presentation 
 I will discuss the need for such rare event simulation methods and will ex
 emplify them on applications such as conformational changes in (signaling)
  proteins\, and amyloid fibril growth. In each case we can gain insight in
  mechanisms of processes that are normally beyond the limit of straightfor
 ward molecular dynamics.  
LOCATION:Department of Chemistry\, Cambridge\, Pfizer lecture theatre
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