Re: CCL:reduced protein models

Masa:
 I am surprised that you did not mention the work of old Moldyn
 (now part of SBI):
 C.E. Padilla, H.E. Alper, D.N. Chin, M. Watanabe, V. Karlov,
 K.B. Blair, H.M. Chun, O. Becker, L. Caves, R. Nagle, M. Karplus,
 and D.N. Haney (2000) J. Comp. Chem., 21(3): 159-184 "A Substructured
 Modeling Approach for Long Time Molecular Dynamics Simulations"
 I think we worked together on some of this, but maybe I am mistaken.
 This work led to a program called MBOND which was sold by MSI.
 I do not know if it is still available.  As you point out, the
 methods are not great, but I think this is partly because they
 are so difficult to use correctly.  However, I think a researcher
 might make some valuable use of the techniques and move them
 forward.
 > Dear Jie,
 >
 > Tremendous efforts have recently been poured into
 > developing a coarse-grain potential for simulating and
 > investigating large biological molecular motions
 > characterized by the long time dynamics. Here are some
 > references that can help you:
 >
 > 1) Troyer et.al. utilize the simple point-per-residue
 > potential developed by Miyazawa & Jernigan to perform
 > the Langevin dynamics. (Check
 > http://www.cmpharm.ucsf.edu/~troyer/eccc/toc.html).
 >
 > 2) The other approaches are to simplify amino acid
 > residues by more than one interaction point;
 >
 > - The Head-Gordon & Brooks approach are described as
 > the Virtual body Dynamics (See Biopolymers, 31, p 77,
 > 1991). In their approach, however, the development of
 > electrostatic potential is not so simple. Therefore,
 > we took their representations of residues and
 > developed our unique potential by defining the pair
 > distribution function, described by Bahar et. al. (See
 > PROTEINS, 29, p292, 1997), from the selected protein
 > molecules. This develop potential was used in the
 > simulation.
 >
 > - Haliloglu and Bahar (See Proteins, 31, p271, 1998)
 > had also utilized their developed a coarse-grain
 > potential for their MD simulations.
 >
 > - The coarser representation of residue is done by
 > Herzyk and Hubbard (See PROTEINS, 17, p310, 1993).
 > They used their residue representations in the content
 > of NMR refinement, but their representation can be
 > utilized to develop unique potential for the dynamics
 > simulation.
 >
 > I myself involved some researches to utilize
 > coarse-grain potential. In my opinion, there are not
 > particularly outstanding coarse-grain potentials yet.
 > Which coarse-grain potential be used in your study
 > truly depends on what level of detail information you
 > want to gain from the simulation. You can also expand
 > the search from the reference presented here.
 >
 > Hopefully, this will help you a bit.
 >
 > Masa Watanabe
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