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Multiple Alignment of protein structures and sequences for VMD
Open accessAbstract
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
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Cited by
Tools for integrated sequence-structure analysis with UCSF Chimera
Meng, E. C., Pettersen, E. F., Couch, G. S., Huang, C. C., & Ferrin, T. E. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-339 · Cited by 732
Ligand-Binding PAS Domains in a Genomic, Cellular, and Structural Context
Henry, J. T., & Crosson, S. (2011) · Annual Review of Microbiology · doi:10.1146/annurev-micro-121809-151631 · Cited by 401
Ames, W., Pantazis, D. A., Krewald, V., Cox, N., Messinger, J., Lubitz, W., & Neese, F. (2011) · Journal of the American Chemical Society · doi:10.1021/ja2041805 · Cited by 289
Essential metabolism for a minimal cell
Breuer, M., Earnest, E. E., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C. A., Smith, H. O., Lapek, J. D., Gonzalez, D. J., et al. (2019) · eLife · doi:10.7554/elife.36842 · Cited by 190
Self-citationCheng, Y., Jin, U.-H., Davidson, L. A., Chapkin, R. S., Jayaraman, A., Tamamis, P., Orr, A., Allred, C., Denison, M. S., Soshilov, A., et al. (2017) · Toxicological Sciences · doi:10.1093/toxsci/kfw230 · Cited by 48
Metadata
- Authors
- Eargle, J., Wright, D., & Luthey-Schulten, Z.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-12-08
- Volume
- 22
- Issue
- 4
- Pages
- 504-506
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2138645972
- Cited by
- 163
- References
- 0
- FWCI
- 1.38
- Type
- journal article
- Language
- en
- Open access
- bronze
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