Computer design yields better, more efficient therapeutic for preventing tissue damage

ree-dimensional structure of Compstatin in solution via nuclear magnetic resonance (NMR) experiments, which he then computationally refined.

The computational de novo protein design system, developed at Princeton University by Floudas and postdoctoral associate John Klepeis, is a technological advance made possible by (i) a novel mixed-integer optimization model that narrows 200 trillion amino acid sequences into a short list of candidates that are likely to produce a peptide of the desired shape, and (ii) a system called ASTRO-FOLD that, using first-principles, predicts the structures that would be formed by the candidate sequences. The second step confirms and refines the first.

A distributed computing environment consisting of eighty Linux-based computers was used for all the computational predictions, and the predicted new peptides were subsequently synthesized and experimentally validated in the Lambris laboratory at Penn.


Contact: Greg Lester
University of Pennsylvania School of Medicine

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