Subject: [Q] On minimal off-lattice models of proteins

From: "Kynn O. Jones" <[email-masked]>
Date: Fri, 18 Sep 1998 17:02:00 -0400 (EDT)

Over the past decade or so, minimal lattice models have been used to
answer fundamental questions about the statistical mechanics of
protein folding.  These models are basically coarse-grained cartoons
of proteins aiming to isolate some fundamental physical features of
the problem.  (For a review, see E. Shakhnovich, "Theoretical studies
of protein folding thermodynamics and kinetics",
Curr. Opin. Struct. Biol. 7:29-40, 1997.)

There have been some published papers on similarly minimalistic
off-lattice models of protein folding, but I have not found much at
all by way of technical modeling details.

I gather that there are two different approaches to modeling proteins
*minimalistically* off-lattice: Monte Carlo and
Brownian/Langevin/noisy dynamics.  How do these approaches compare?
Naively, I would have assumed that MC would be computationally faster;
hence I don't quite understand why people bother with BD for this sort
of modeling.  (One possibility that occurs to me is that BD may be
considered more convincing as a model of specific kinetic details, as
opposed to merely a means to sample conformational space; or maybe
off-lattice MC requires much more parameter tweaking to get it to work
than BD.)

I would appreciate opinions from those familiar with the ins and outs
of both techniques (particularly within the context of minimal protein
models).  Has anyone reviewed in print the relative merits of
off-lattice MC vs. BD?

I'll post a summary of the responses I get.

Thanks in advance,

KJ
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