Multiple Alignment of protein structures and sequences for VMD

Multiple Alignment is a new interface for performing and analyzing multiple protein structure alignments. It enables viewing levels of sequence and structure similarity on the aligned structures and performing a variety of evolutionary and bioinformatic tasks, including the construction of structure-based phylogenetic trees and minimal basis sets of structures that best represent the topology of the phylogenetic tree. It is implemented as a plugin for VMD (Visual Molecular Dynamics), which is distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics at the University of Illinois. Availability: Both binary and source code downloads for VMD 1.83, which includes Multiple Alignment, are available from http://www.ks.uiuc.edu/Research/vmd/. The Multidimensional QR factorization algorithm is available at http://www.scs.uiuc.edu/~schulten/software.html Contact: multiseq@scs.uiuc.edu