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Fusion Protein MODeller (FPMOD)

FPMOD is a computational tool to predict FRET efficiency changes by constructing FRET biosensors and sampling their conformational space through rigid-body rotation. FPMOD consists of a set of programs to generate fusion protein constructs from PDB files, define regions of flexible linkers between domains and produce random conformations by rotation of domains around these flexible linkers. For each conformation generated, the distance and orientation factors, as well FRET efficiencies are then calculated. A tabulation of these values can be used to predict FRET changes of biosensor designs.

Perl scripts were written to determine FRET from generated conformations. ActivePerl for Windows XP needs to be installed to run these scripts.

FPGA-accelerated Smith-Waterman algorithm

The Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences used to infer sequence homology. Using FPGA-based hardware, this algorithm was accelerated by up to 160 folds compared to a pure software implementation running on the same FPGA with a Altera Nios II softprocessor. This design of FPGA accelerated hardware offers a new promising direction to seeking computation improvement of genomic database searching.

Monte Carlo Biomolecular Simulator

Deciphering and designing complex biomolecular networks in the cell are the goals of systems and synthetic biology, respectively. The effects of localization, spatial heterogeneity and molecular fluctuations in biomolecular networks are not well understood. Using a theoretical approach based on physical principles, a computational tool named Monte Carlo Biomolecular Simulator (MBS) was developed, enabling studies of biomolecular kinetics with both spatial and temporal resolutions.

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