Lattice Microbes
Lattice Microbes is a software package for efficiently sampling trajectories from the chemical and reaction-diffusion master equations (CME/RDME) on high performance computing (HPC) infrastructure using both exact and approximate methods.
For more information, see the Lattice Microbes home page.
Representative papers related to Lattice Microbes:
Elijah Roberts, John E Stone, and Zaida Luthey-Schulten.
Lattice Microbes: high-performance stochastic simulations of the reaction-diffusion master equation
Submitted.
E. Roberts, A. Magis, J.O. Ortiz, W. Baumeister, and Z. Luthey-Schulten
Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
PLoS. Comput. Biol., 7(3):e1002010, 2011
E. Roberts, J.E. Stone, L. Sepulveda, W.W. Hwu, and Z. Luthey-Schulten
Long time-scale simulations of in vivo diffusion using GPU hardware
In Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009
MultiSeq 2.0
MultiSeq is an extension to VMD that provides a combined sequence and structure bioinformatics analysis environment. VMD and MultiSeq are available for many platforms, including Windows, Mac OS X, Linux, and Solaris. They can be downloaded from the NIH Resource for Macromolecular Modeling and Bioinformatics. Tutorials are also available for learning how to use MultiSeq and VMD.
For more information, see the MultiSeq home page.
Representative papers related to MultiSeq:
E. Roberts, J. Eargle, D. Wright, and Z. Luthey-Schulten. MultiSeq: Unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics, 7:382, 2006.
J. Eargle, D. Wright, and Z. Luthey-Schulten. Multiple Alignment of protein structures and sequences for VMD. Bioinformatics, 22:504, 2006.
SeqQR 1.0.1
Sequence QR (SeqQR) is a program that generates a nonredundant set of proteins that represents the topology of the molecular phylogenetic tree of the homologous group.
SeqQR is available on the following platforms:
Representative papers related to SeqQR:
A. Sethi, P. O'Donoghue, and Z. Luthey-Schulten. Evolutionary profiles from the QR factorization of multiple sequence alignments. PNAS, 102:4045, 2005.
P. O'Donoghue and Z. Luthey-Schulten, Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information. J. Mol. Biol., 346:875, 2005.
P. O'Donoghue, and Z. Luthey-Schulten. On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol. Mol. Biol. Rev., 67:550, 2003.
Tessellator 1.0
Tessellator is an application for the tessellation of 3D volume in and around biological molecules. It creates Tcl script files which are run within VMD to visualize volumes in context with their associated molecular structures.
For help with installation and use of Tessellator, click here.
For supplementary material associated with the paper "Visualizing the Dual Space of Biological Molecules", click here.
Tessellator is available on the following platforms:
Representative paper related to Tessellator:
J Eargle, and Z. Luthey-Schulten, Visualizing the Dual Space of Biological Molecules. Comp. Biol. Chem., 30:219, 2006.
