Browse Prior Art Database

1/R**4 Shape Envelope for Macromolecules

IP.com Disclosure Number: IPCOM000106010D
Original Publication Date: 1993-Sep-01
Included in the Prior Art Database: 2005-Mar-20
Document File: 2 page(s) / 67K

Publishing Venue

IBM

Related People

Pickover, CA: AUTHOR

Abstract

Disclosed is a computer graphics method for computing a bounding envelope around a macromolecule in order to help the human viewer see global features. The graphical bounding envelope is not the standard envelope based on voltage potential or other electrostatic considerations.

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1/R**4 Shape Envelope for Macromolecules

      Disclosed is a computer graphics method for computing a
bounding envelope around a macromolecule in order to help the human
viewer see global features.  The graphical bounding envelope is not
the standard envelope based on voltage potential or other
electrostatic considerations.

      The remarkable ease with which this computational method
highlights the overall shape of a molecule, particularly when coupled
with IBM* products such as Data Explorer, makes the method of
particular interest.  The determination of global shape is an active
area of interest, particularly in studies of proteins and drugs.

      Often by looking at an entire macromolecule represented by
thousands of atoms, the human eye has difficulty in seeing grooves,
clefts, and pockets -- structural features which are often relevant
biologically.  To overcome this, a "shape envelope" is displayed by
computing the distance of the centers of every atoms and summing them
with an
 1/ r sup 4 dependence.  Disclosed is the use of:
rho (x vector ) = sum from i a delta (x vector - x vector sub i )
                                                                  (1)
to represent a collection of points.

I (x vector ) = sum from i a over <vbar x vector - x vector sub i
vbar
 sup alpha >
                                                                  (2)
where
 a = 1.  This is a much simpler expression than those used for
realistic voltage potential equations for molecules, but when
 alpha = 1 ,
 I is the voltage potential for a collection of point charges.  Here
 rho is simply the value 1 at specified coordinates of points in
space.  Eq.  2 defines a global geometrical envelope which is useful
for scientific visualization.  In a computer program, one can
represent the "internal skeletal structure" of a molecule by a
collection of points
 j .
 I sub i is subsequently obtained by computing
 sum from  j 1 / d...