Work

Multiple Alignment of protein structures and sequences for VMD

Year: 2005

Type: article

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. Availability: Both binary and source code downloads for VMD 1.83, which includes Multiple Alignment, are available from . The Multidimensional QR factorization algorithm is available at Contact: [email protected]

Source: Bioinformatics

DOI: 10.1093/bioinformatics/bti825

Authors: John Eargle, Dan Wright, Zaida Luthey-Schulten

Institution: University of Illinois Urbana-Champaign

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Institutes of Health, National Institute of General Medical Sciences, National Center for Research Resources

Awards: An Institutional NRSA in Molecular Biophysics, RESOURCE FOR MACROMOLECULAR MODELING AND BIOINFORMATICS