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. |
 |
|
|
MultiSeq 2.0
MultiSeq is an extension to VMD that
provides a combined sequence and structure bioinformatics analysis environment. For more information, see the MultiSeq home page. 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.
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
|
 |
|
|
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
|
 |
|
|
