FADE and PADRE
- Detailed Technology 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/
- Others
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Tech ID/UC Case
19309/2002-817-0
Related Cases
2002-817-0
- *Abstract
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None
- *Principal Investigator
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Name: Julie Mitchell
Department:
Name: Lynn Ten Eyck
Department:
- Country/Region
- USA
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