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Description: University researchers
have invented a powerful method for the molecular modeling
of proteins. This invention can rapidly calculate the
distribution of atomic neighbors. A primary advantage
of this atomic density method is its computational efficiency,
especially over previous generation method that use
Fast Fourier Transforms. Software based on this algorithm
can analyze molecular shape in seconds, while other
methods may take minutes or hours.
This algorithm can be used to deduce surface shape
features, such as crevices and protrusions. It can also
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 the study of protein
structure-function relationships..
Keywords: bioinformatics, molecular simulation, protein
structure evaluation, general atomic density calculations
Case Number: SD2003-027
Inquiries To: invent@ucsd.edu
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