Molecular Dynamics Simulation for Drug Design

comparison of x-ray structures (blue)results of MD simulation (red) of villin (A) and FiP35 (B).


In a preview of his upcoming keynote at CHI (Cambridge Healthtech Institute) and Bio-IT World’s Eleventh Annual Structure-Based Drug Design conference, David E. Shaw, Chief Scientist of D. E. Shaw Research, talks with Bio-IT World editor Kevin Davies about a specialized supercomputer, called Anton, that has simulated the behavior of proteins for periods as long as two milliseconds. Excerpts from some of these simulations, showing events such as drugs finding their own binding sites, will be shown during his upcoming keynote address – “Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine.”

As a sneak preview to the keynote, the Podcast “Anton: Molecular Dynamics Simulation for Drug Design” is available for download at, for full details see

In the podcast, D.E. Shaw discusses the combination of improvements in hard- and software that enabled them to go for such long simulations – “… many of the kinds of phenomena that are most interesting from the viewpoint of drug binding take place over longer timescales than was previously possible, even on the worlds fastest supercomputers to simulate“. The co-development of algorithms and specialised hardware results in Anton being a machine that is “so highly specialised that it wouldn’t be very useful for pretty much anything else“.

The podcast-links were posted on LinkedIn by James Prudhomme, Marketing Manager at Cambridge Healthtech Institute (CHI), hence this post should be marked as “advertisement” and treated (pretty much like anything else) with caution and a criticial mind. On the latter, I recommend Bosco’s excellent article “Thousands of hours of Molecular Dynamics saves you minutes of a Monte Carlo calculation” and more recently, “Purity in the atomic force-fields of molecular dynamics simulations“.

References: Here is a link to the article in science
Science 15 October 2010: Vol. 330 no. 6002 pp. 341-346 DOI: 10.1126/science.1187409

and to the full list of D.E. Shaw publications

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