DOI: 10.1093/bioinformatics/bti825. <i>Multiple Alignment</i> of protein structures and sequences for VMD

Multiple Alignment of protein structures and sequences for VMD

10.1093/bioinformatics/bti825

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

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: multiseq@scs.uiuc.edu

Bibliography

Eargle, J., Wright, D., & Luthey-Schulten, Z. (2005). Multiple Alignment of protein structures and sequences for VMD. Bioinformatics, 22(4), 504â506.

Authors 3

John Eargle (first)
Dan Wright (additional)
Zaida Luthey-Schulten (additional)

References 12 Referenced 143

10.1093/nar/25.17.3389 / Nucleic Acids Res. / Gapped BLAST and PSI-BLAST: a new generation of protein database search programs by Altschul (1997)
10.1093/nar/28.1.254 / Nucleic Acids Res. / The ASTRAL compendium for sequence and structure analysis by Brenner (2000)
10.1093/nar/22.22.4673 / Nucleic Acids Res. / CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice by Higgins (1994)
10.1016/0263-7855(96)00018-5 / J. Mol. Graph. / VMD–Visual Molecular Dynamics by Humphrey (1996)
10.1002/pro.5560071126 / Protein Sci. / HOMSTRAD: a database of protein structure alignments for homologous families by Mizuguchi (1998)
10.1016/S0022-2836(05)80134-2 / J. Mol. Biol. / SCOP: a structural classification of proteins database for the investigation of sequences and structures by Murzin (1995)
10.1128/MMBR.67.4.550-573.2003 / Microbiol. Mol. Biol. Rev. / On the evolution of structure in aminoacyl-tRNA synthetases by O'Donoghue (2003)
10.1016/j.jmb.2004.11.053 / J. Mol. Biol. / Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information by O'Donoghue (2005)
10.1073/pnas.0509617102 / Proc. Natl. Acad. Sci. USA / The Evolutionary History of Cys-tRNA(Cys) formation by O'Donoghue (2006)
10.1002/prot.340140216 / Proteins / Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels by Russell (1992)
10.1073/pnas.0409715102 / Proc. Natl Acad. Sci. USA / Evolutionary profiles from the QR factorization of multiple sequence alignments by Sethi (2005)
10.1093/bioinformatics/17.4.375 / Bioinformatics / PALI: a database of alignments and phylogeny of homologous protein structures by Sujatha (2001)

Dates

Type	When
Created	19 years, 8 months ago (Dec. 8, 2005, 8:43 p.m.)
Deposited	2 years, 7 months ago (Jan. 24, 2023, 4:17 a.m.)
Indexed	6 days, 16 hours ago (Aug. 26, 2025, 2:45 a.m.)
Issued	19 years, 8 months ago (Dec. 8, 2005)
Published	19 years, 8 months ago (Dec. 8, 2005)
Published Online	19 years, 8 months ago (Dec. 8, 2005)
Published Print	19 years, 6 months ago (Feb. 15, 2006)

Funders 0

None

BibTeX

@article{Eargle_2005, title={Multiple Alignment of protein structures and sequences for VMD}, volume={22}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/bti825}, DOI={10.1093/bioinformatics/bti825}, number={4}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Eargle, John and Wright, Dan and Luthey-Schulten, Zaida}, year={2005}, month=dec, pages={504–506} }

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