monte carlo algorithm for protein folding

Kevin Karplus karplus at bray.cse.ucsc.edu
Mon Oct 27 13:50:49 EST 2003


In article <29b47968.0310211348.5fa4673d at posting.google.com>, 
	Tzuriel Cohen wrote:
> 1)does anyone know where i can get the algorithm of Monte Carlo for
> protein
> folding ?? 
> i need to write a program doing this on a lattice model.

"Protein folding" and "lattice model" are almost mutually contradictory.
Once you reduce yourself to a lattice model, you are no longer doing
anything very protein-like.  Some biophysics people have used lattice
models to see what happens in simplified systems, since real proteins
are too complex, but their results can hardly be called protein folding.

A Monte Carlo algorithm is simply one in which randomness plays a
major role.  There is no single "Monte Carlo" algorithm.

> 2)does any one know about a free website doing MonteCarlo simulation
> for protein folding on sequences ??

I don't know of any free Monte Carlo web services for proteins, as
Monte Carlo simulation is, by its very nature, rather compute
intensive. 


-- 
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Professor of Computer Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
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