Software
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.
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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