Protein MODeller (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.
Windows XP version 2 (June 13, 2007): Download
Perl scripts were written to determine FRET from generated conformations. ActivePerl for Windows XP needs to be installed to run these scripts.
Perl scripts version 1 (June 22, 2007): Download
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.
Quartus files (June 7, 2007): Download
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.
Windows XP version 1 (September 5, 2007): Download