Method for Fast Atomic Density Evaluation

Technology 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