Fast Atomic Density Evaluator (FADE)

and

Pairwise Atomic Density Reverse Engineering (PADRE)

Abstract | Download | References

Abstract

The Fast Atomic Density Evaluator (FADE) and Pairwise Atomic Density Reverse Engineering (PADRE) programs are designed to aid in the molecular modeling of proteins. In particular, the programs can rapidly elucidate features of interest such as crevices, grooves and protrusions. The topographical information produced by FADE and PADRE can help researchers easily pinpoint the most prominent features of a protein, regions which are likely to participate in interactions with other molecules. In addition to providing shape descriptors to aid in analyzing single molecules, FADE can directly evaluate the level of shape complementarity for docked protein-protein complexes.

If you are interested in analyzing a protein-protein or protein-DNA interface, we recommend you use the new KFC Server

We also recommend checking out the Crevasse program by Elaine Thompson and Lynn Ten Eyck at UCSD, which uses data from FADE to locate crevices on the surface of a protein. Crevasse is available for download here.

FADE Images

PADRE Images

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By having FADE and PADRE users fill out this form we obtain information requested by our funding agencies, so please provide us with accurate information. We also enjoy seeing the different countries and institutions our users come from.

FADE and PADRE are free for non-commercial use only.

References

[1] Mitchell, J.C., Kerr, R. and Ten Eyck, L.F., Rapid atomic density measures for molecular shape characterization, J. Mol. Graph. Model. 19(3): 325-330, 2001.