Subject: Request for comment: interest in various comp chem capabilities

From: Hon M Chun <[email-masked]>
Date: Wed, 3 Feb 1999 14:50:48 -0500

Dear netters,

	I'd like to get some feedback on the level of interest in the
following topics. The purpose of this request is to gather information that
will allow Moldyn to determine what features to incorporate into potential
future products.

*	Free energy from MD calculations
How practical are these calculations perceived to be, compared to the
alternatives? Is the accuracy mostly limited by the forcefield parameter
set, or by the length of the simulation trajectory?

*	High throughput molecular dynamics
High throughput screening and docking of molecules are commonplace. How
about high throughput molecular dynamics of the docked compounds (ligand and
protein)? How important is it to analyze dynamic motions of the docked
ligand/receptor complexes?

*	Coarse-grained dynamics modeling of large macromolecules, such as
viral capsids
How much interest is there for a coarse-grained modeling approach for the
dynamics of large macromolecules that can be completed in a reasonably short
amount of time? By coarse-grained, I mean grouping together atoms at the
sub-residue level, residue level, or beyond.  We therefore sacrifice many
atomic details for greater speed and access to larger scale properties.
Interaction forces are calculated at corresponding levels, and not at the
atomistic level, resulting in significantly higher computational speed
(approximately 2 orders of magnitude faster) than atomistic models. Such a
dynamics model will not include explicit solvent, but will implicitly
include solvent in the parameter set or via some form of continuum model. I
recognize that there are many groups that are developing this class of
simulation methods. I'd like to hear from potential users of such methods,
to gauge the level of commercial and academic interest.

*	Dynamics of Self-assembly
How much interest is there in studying the assembly or aggregation process?
Would you use it for nanotechnology or molecular biology?

Thank you in advance for your comments.

Hon Chun
[email-masked]

Hon M. Chun, Ph.D.
Vice President & Chief Technical Officer
Moldyn, Inc., 955 Massachusetts Avenue, Cambridge, MA 02139-3180
Phone:(617)354-3124 Voicemail: X16, Fax:(617)491-4522