Protein interaction & molecular dynamics

Andrew Martin martin at
Wed Jul 17 15:51:21 EST 1996

Martin Jones (mlj at wrote:
: Antonio Rosato (antonio at wrote:
: : Dear all,
: : I would like to know whether there are programs available (free or 
: : commercial) that can simulate protein interaction through molecular
: : dynamics. Should such a program be based on brownian dynamics?
: : Suitable protocols for 'ordinary' molecular dynamics programs
: : (AMBER,CHARMM..) are welcome as well.
: : Thanks a lot!
: : Antonio

: : e-mail: antonio at

: Unfortunately usable step-sizes in molecular dynamics simulations are measured 
: in picoseconds. & each step takes at least a few seconds to simulate. 

: So unless you are willing to wait several times the lifetime 
: of the universe I'm afraid you'll find that current molecular dynamics 
: techniques aren't up to this. If you already know the structure of a
: protein complex at the moment of interaction you _might_ be able to 
: gain some useful information on the low-level detail of that interaction
: using MD, but if you're thinking about just setting a couple of copies of 
: protein & substrate up in a box of waters & seeing what happens then I 
: suggest that you not wait up for the results :)

: Martin.

Actually it's been done quite successfully using Monte Carlo techniques
(the ICM program from Ruben Abagyan) and there were attempts some years
ago to use a modified CHARMM. As I remember, this was done by Bernie
Brooks. He simulated the two molecules in reasonable proximity and
watched the sidechains move. He then fitted the original structure to
the moved sidechains and repeated. Gradually the structures moved
towards one another. My apologies if I have the details wrong...


Dr. Andrew C.R. Martin,         University College London & SciTech Software
EMAIL: martin at                Tel:(Work) +44(0)171 419 3890
URL:          (Home) +44(0)1372 275775

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