MUSTANG: a multiple structural alignment algorithm
- PMID: 16736488
- DOI: 10.1002/prot.20921
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(alpha) 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.
Similar articles
-
CAALIGN: a program for pairwise and multiple protein-structure alignment.Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):514-25. doi: 10.1107/S0907444907000844. Epub 2007 Mar 16. Acta Crystallogr D Biol Crystallogr. 2007. PMID: 17372357
-
An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments.J Mol Biol. 2000 Aug 18;301(3):691-711. doi: 10.1006/jmbi.2000.3975. J Mol Biol. 2000. PMID: 10966778
-
Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.Proteins. 1992 Oct;14(2):309-23. doi: 10.1002/prot.340140216. Proteins. 1992. PMID: 1409577
-
Protein multiple sequence alignment.Methods Mol Biol. 2008;484:379-413. doi: 10.1007/978-1-59745-398-1_25. Methods Mol Biol. 2008. PMID: 18592193 Review.
-
Multiple sequence alignment.Curr Opin Struct Biol. 2006 Jun;16(3):368-73. doi: 10.1016/j.sbi.2006.04.004. Epub 2006 May 5. Curr Opin Struct Biol. 2006. PMID: 16679011 Review.
Cited by
-
Accurate prediction of the dynamical changes within the second PDZ domain of PTP1e.PLoS Comput Biol. 2012;8(11):e1002794. doi: 10.1371/journal.pcbi.1002794. Epub 2012 Nov 29. PLoS Comput Biol. 2012. PMID: 23209399 Free PMC article.
-
Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity.Int J Biol Macromol. 2022 Dec 1;222(Pt B):2467-2478. doi: 10.1016/j.ijbiomac.2022.10.031. Epub 2022 Oct 8. Int J Biol Macromol. 2022. PMID: 36220405 Free PMC article.
-
Quality Assessment of Selected Protein Structures Derived from Homology Modeling and AlphaFold.Pharmaceuticals (Basel). 2023 Nov 29;16(12):1662. doi: 10.3390/ph16121662. Pharmaceuticals (Basel). 2023. PMID: 38139789 Free PMC article.
-
Structural characterization of the mechanism through which human glutamic acid decarboxylase auto-activates.Biosci Rep. 2013 Jan 11;33(1):137-44. doi: 10.1042/BSR20120111. Biosci Rep. 2013. PMID: 23126365 Free PMC article.
-
Environmental selection pressures related to iron utilization are involved in the loss of the flavodoxin gene from the plant genome.Genome Biol Evol. 2015 Feb 16;7(3):750-67. doi: 10.1093/gbe/evv031. Genome Biol Evol. 2015. PMID: 25688107 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
