Engineered proteins are synthetic novel proteins (not found in nature) that are designed to fulfill a predetermined biological function. Such proteins can be used as molecular markers, inhibitory agents, or drugs. For example, a synthetic protein could bind to a critical protein of a pathogen, thereby inhibiting the function of the target protein and potentially reducing the impact of the pathogen. In this paper we present the In-Silico Protein Synthesizer (InSiPS), a massively parallel computational tool for the IBM Blue Gene/Q that is aimed at designing inhibitory proteins. More precisely, InSiPS designs proteins that are predicted to interact with a given target protein (and may inhibit the target's cellular functions) while leaving non-target proteins unaffected (to minimize side-effects). As proof-of-concepts, two InSiPS designed proteins have been synthesized in the lab and their inhibitory properties have been experimentally verified through wet-lab experimentation.

Additional Metadata
Keywords applications, bioinformatics and computational biology, computational medicine and bioengineering, protein design, synthetic biology
Persistent URL dx.doi.org/10.1145/2807591.2807630
Conference International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2015
Citation
Schoenrock, A. (Andrew), Burnside, D. (Daniel), Moteshareie, H. (Houman), Wong, A, Golshani, A, Dehne, F, & Green, J. (2015). Engineering inhibitory proteins with InSiPS: The in-silico protein synthesizer. Presented at the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2015. doi:10.1145/2807591.2807630