Explore

J. Michael Cherry Cherry at Coffee.MGH.Harvard.EDU
Thu Sep 27 11:40:40 EST 1990


In article <3137 at bruce.cs.monash.OZ.AU> lloyd at bruce.cs.monash.OZ.AU (lloyd 
allison) writes:
> This is to request references to a package called Explore (sp?)
> that predicts protein tertiary structure.
> 
> Lloyd Allison           
> Department of Computer Science  UUCP:   lloyd at bruce.cs.monash.edu.au

Sounds like you are referring to a program originally from Axel Brunger
while at Harvard, now at U of Chicago I believe.  See A.  Brunger, Acta
Cryst.  A, A46, 46-57 (1990).  This program like other programs from
Karplus' group at Harvard are commercialized by Polygen Corp in Waltham,
Massachusetts (617) 890-2888.  The introduction on the X-PLOR product
sheet says:

"X-PLOR (tm) is a macromolecular crystal structure program
which integrates x-ray diffraction data with molecular
mechanics, dynamics, energy minimization, or NMR internuclear
distances to aid in the solution of 3-dimensional molecular
structures. The technique of simulated annealing overcomes
local misplacement of flexible fragments. X-PLOR uses the
CHARMm (tm) force field, modified automatically for use in
high temperature dynamics simulations. The QUANTA (tm) 
Structure Analysis and Refinement modeling application
package facilitates access to and data exchange between
X-PLOR and QUANTA."

X-PLOR is not meant to generate a folded protein structure from just the
primary amino acid sequence. It requires structural data like an electron
density map or NMR measurements as its reference. It then manipulates the
coordinates to fit the structural data, as opposed to CHARMm which is 
generally used to fit structures to an energy function.

I have no connection to Polygen Corp. I am not even a satisfied user.

Mike Cherry
cherry at frodo.mgh.harvard.edu
Department of Molecular Biology
Massachusetts General Hospital, Boston




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