Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz,
James C. Phillips, Fangqiang Zhu, and Klaus Schulten.
Large scale simulation of protein mechanics and function.
In Frederic M. Richards, David S. Eisenberg, and John Kuriyan,
editors, Advances in Protein Chemistry, volume 66, pp. 195-247.
Elsevier Academic Press, New York, 2003.
TAJK2003
The biomedical sciences are enjoying a wealth of data from
innovative new techniques in structure determination, DNA
sequencing at the level of entire genomes, and direct manipulation
and observation of single molecules. Computational biologists
seek to extend and refine these experimental advances through
atomic level modeling, often in direct collaboration with
experimental researchers. Systems that capture the interest of
experimental and computational biologists today are membrane
channels, bioenergetic proteins like ATPase, or the machinery of
the expression system like the ribosome, all of which should be
simulated in realistic environments. Combining expertise from the
physical, computational and life sciences, computational biologists
have developed for this purpose modeling tools for biomolecular
systems of 100,000 atoms and more. They have also advanced
mathematical modeling using stochastic and non-equilibrium
statistical mechanical methods to bridge the still huge gap
between simulation (10ns) and physiological times (1ms). This
article demonstrates some of the progress achieved so far and the
discoveries made.
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