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Description: University researchers
have written powerful software for the molecular modeling
of protein.
The Fast Atomic Density Evaluation (FADE) and Pairwise
Atomic Density Reverse Engineering (PADRE) programs
deduce molecular shape using the local density of atoms
at points within a few Angstroms of the molecular surface.
FADE uses Fast Fourier Transforms and convolution integrals
to rapidly calculate the distribution of atomic neighbors.
PADRE poses the question of atomic density as an inverse
problem based on a one-dimensional integral of Lennard-Jones
potentials. A primary advantage of atomic density methods
is their computational efficiency. FADE can analyze
molecular shape in seconds, while other methods may
take minutes or hours.
FADE and PADRE can deduce surface shape features, such
as crevices and protrusions. FADE is also able to do
detailed analysis of shape complementarity for docked
complexes. The ability to determine regions of strong
shape match or mismatch in an interface is very useful
to computer-aided drug design. In addition to research,
atomic density methods offer an ideal tool for learning
about the shape features of molecules. The basic ideas
underlying density methods can be understood intuitively,
and integration within existing packages for molecular
visualization would be a great aid to students studying
protein structure-function relationships.
For more information please see the website http://www.sdsc.edu/CCMS/FP/
Keywords: bioinformatics, molecular
simulation
Case Number: SD2002-817
Inquiries To: invent@ucsd.edu
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