Subject: Summary: Reduced Protein Models

From: "J. Zheng" <[email-masked]>
Date: Fri, 12 Apr 2002 11:15:30 -0700 (PDT)

Dear CCLer:

> >   I have a general question about the protein simulation. For protein
> > simulation, force field is important issue. As I know as far, most of
> > persons use different force fields such as Charmm, Gromas, Amber etc
> > to describe different protein systems with all-atoms model.
> >
> >   Sometimes protein is so huge that we have to consider another way to
> > deal with it. For example, we introduce new algorithm (Cell multipole
> > method, PPPM) to reduce computation time, or we resort to parallel
> > program.  I am curious that does anyone has develop the general force
> > field (epslo, sigma, charge) for only 20 acid amio residues if we
> > treat each residue as one atom.  If yes, could you please give me a
> > reference paper?

---------------------------------------------------------------------------
1. Tommi Hassinen <[email-masked]>

   Hassinen T.; Perdkyld M. J Comput Chem 22, 1229-1242 (2001)

I have used 1-3 mass points / amino acid residue, and a solvent-accessible
surface based solvation model. The program is also available (with source
code) at

   http://www.bioinformatics.org/ghemical

-----------------------------------------------------------------------------
2. Konrad Hinsen <[email-masked]>

A simple harmonic forcefield for a one-particle-per-residue model is
described in the following paper:
  K. Hinsen, A.J. Petrescu, S. Dellerue, M.C. Bellissent-Funel, G.R.
Kneller Harmonicity in slow protein dynamics
  Chem. Phys. 261, 25-37 (2000)

The paper also shows that this forcefield plus harmonic Brownian dynamics
(Brownian modes) gives excellent results for dynamic quantities
(correlation functions) over a large time range. An implementation of this
technique is available in the Molecular Modelling Toolkit, to be found at

  http://dirac.cnrs-orleans.fr/MMTK/

--------------------------------------------------------------------------------
3. Richard Gillilan <[email-masked]>

 "Energy-based de novo protein folding by conformational
  space annealing and an off-lattice united-residue force
  field: Application to the 10-55 fragment of staphylococcal
  protein A and to apo calbindin D9K"

  P NATL ACAD SCI USA 96 (5): 2025-2030 MAR 2 1999

I also remember a paper by T. Head-Gordon & Brooks in which residues are
treated as multipoles: BIOPOLYMERS 31 (1): 77-100 JAN 1991

-----------------------------------------------------------------------------------
4. Masakatsu Watanabe <[email-masked]>

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.

-------------------------------------------------------------------------------
5. Dr. David N. Haney <[email-masked]>

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 really appreciate for your helping.

 Jie