The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
MUSTANG: A multiple structural alignment algorithm
Abstract
Multiple structural alignment is a fundamental problem in structural genomics. In this article, we define a reliable and robust algorithm, MUSTANG (MUltiple STructural AligNment AlGorithm), for the alignment of multiple protein structures. Given a set of protein structures, the program constructs a multiple alignment using the spatial information of the C α atoms in the set. Broadly based on the progressive pairwise heuristic, this algorithm gains accuracy through novel and effective refinement phases. MUSTANG reports the multiple sequence alignment and the corresponding superposition of structures. Alignments generated by MUSTANG are compared with several handcurated alignments in the literature as well as with the benchmark alignments of 1033 alignment families from the HOMSTRAD database. The performance of MUSTANG was compared with DALI at a pairwise level, and with other multiple structural alignment tools such as POSA, CE‐MC, MALECON, and MultiProt. MUSTANG performs comparably to popular pairwise and multiple structural alignment tools for closely related proteins, and performs more reliably than other multiple structural alignment methods on hard data sets containing distantly related proteins or proteins that show conformational changes. Proteins 2006. © 2006 Wiley‐Liss, Inc.
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Protein Structure Comparison by Alignment of Distance Matrices
Holm, L., & Sander, C. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1489 · Cited by 3,984 · cited 1×
“DALI, which compares distance maps, is the most popular and widely used pairwise structural alignment tool.(12) (See Koehl(30) for a review.”
MethodThe relation between the divergence of sequence and structure in proteins.
Chothia, C., & Lesk, A. M. (1986) · The EMBO Journal · doi:10.1002/j.1460-2075.1986.tb04288.x · Cited by 2,458
Self-citationDIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern, B. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.211 · Cited by 678
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Comparative Protein Structure Modeling Using Modeller
Eswar, N., Webb, B., Marti‐Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Sali, A. (2006) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0506s15 · Cited by 4,478
Comparative Protein Structure Modeling Using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.3 · Cited by 4,316
PROMALS3D: a tool for multiple protein sequence and structure alignments
Pei, J., Kim, B.-H., & Grishin, N. V. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn072 · Cited by 1,298
Comparative protein structure modeling using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Protein Science · doi:10.1002/cpps.20 · Cited by 730
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
Zhang, C., Shine, M., Pyle, A. M., & Zhang, Y. (2022) · Nature Methods · doi:10.1038/s41592-022-01585-1 · Cited by 511
Metadata
- Authors
- Konagurthu, A. S., Whisstock, J. C., Stuckey, P. J., & Lesk, A. M.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2006-05-30
- Volume
- 64
- Issue
- 3
- Pages
- 559-574
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2031901496
- Cited by
- 713
- References
- 7
- FWCI
- 13.63
- Type
- journal article
- Language
- en
- Open access
- closed
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