Multiple Alignment of protein structures and sequences for VMD.

John Eargle; Dan Wright; Zaida Luthey-Schulten

doi:10.1093/bioinformatics/bti825

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Multiple Alignment of protein structures and sequences for VMD.

John Eargle·Dan Wright·Zaida Luthey-Schulten

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Abstract

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.

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Amino Acid Sequence Computer Graphics Computer Simulation Models, Chemical Models, Molecular Molecular Sequence Data Protein Conformation Proteins Sequence Alignment Sequence Analysis, Protein Software User-Computer Interface Journal Article Research Support, N.I.H., Extramural

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John Eargle, Dan Wright, Zaida Luthey-Schulten. 2005-12-08. Multiple Alignment of protein structures and sequences for VMD.. https://doi.org/10.1093/bioinformatics%2Fbti825

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