The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
Flexible structure alignment by chaining aligned fragment pairs allowing twists
Abstract
Motivation: Protein structures are flexible and undergo structural rearrangements as part of their function, and yet most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment. Results: We have developed the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT), a new method for structural alignment of proteins. The FATCAT approach simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference protein. In contrast, currently existing flexible structure alignment programs treat the hinge detection as a post-process of a standard rigid body alignment. We illustrate the advantages of the FATCAT approach by several examples of comparison between proteins known to adopt different conformations, where the FATCAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges. Contacts: adam@burnham.org *To whom correspondence should be addressed.
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Murzin, A. G., Brenner, S. E., Hubbard, T., & Chothia, C. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80134-2 · Cited by 6,445
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 5×
“, 1996) and compared its performance with three rigid alignment programs, DALI (Holm and Sander, 1993), VAST (Madej et al.”
BackgroundMethodResultInfluentialProtein structure alignment by incremental combinatorial extension (CE) of the optimal path
Shindyalov, I. N., & Bourne, P. E. (1998) · Protein Engineering Design and Selection · doi:10.1093/protein/11.9.739 · Cited by 2,041
Principles of protein structure
(1980) · Journal of Steroid Biochemistry · doi:10.1016/0022-4731(80)90019-9 · Cited by 1,058
Structural Mechanisms for Domain Movements in Proteins
Gerstein, M., Lesk, A. M., & Chothia, C. (1994) · Biochemistry · doi:10.1021/bi00188a001 · Cited by 744
Protein flexibility predictions using graph theory
Jacobs, D. J., Rader, A. J., Kuhn, L. A., & Thorpe, M. F. (2001) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.1081 · Cited by 727
Threading a database of protein cores
Madej, T., Gibrat, J., & Bryant, S. H. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340230309 · Cited by 440
Wriggers, W., & Schulten, K. (1997) · Proteins: Structure, Function, and Genetics · doi:10.1002/(sici)1097-0134(199709)29:1<1::aid-prot1>3.0.co;2-j · Cited by 256
Structural and Functional Aspects of Domain Motions in Proteins
Bennett, W. S., Huber, R., & Engel, J. (1984) · Critical Reviews in Biochemistry · doi:10.3109/10409238409117796 · Cited by 245
Structure Comparison and Structure Patterns
Eidhammer, I., Jonassen, I., & Taylor, W. R. (2000) · Journal of Computational Biology · doi:10.1089/106652701446152 · Cited by 212
Cited by
One core, two shells: bacterial and eukaryotic ribosomes
Melnikov, S., Ben-Shem, A., Garreau de Loubresse, N., Jenner, L., Yusupova, G., & Yusupov, M. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2313 · Cited by 477
FATCAT 2.0: towards a better understanding of the structural diversity of proteins
Li, Z., Jaroszewski, L., Iyer, M., Sedova, M., & Godzik, A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa443 · Cited by 231
Self-citationCrystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism
Li, F., Liu, J., Zheng, Y., Garavito, R. M., & Ferguson-Miller, S. (2015) · Science · doi:10.1126/science.1260590 · Cited by 163
Multi-omic data integration enables discovery of hidden biological regularities
Ebrahim, A., Brunk, E., Tan, J., O'Brien, E. J., Kim, D., Szubin, R., Lerman, J. A., Lechner, A., Sastry, A., Bordbar, A., et al. (2016) · Nature Communications · doi:10.1038/ncomms13091 · Cited by 155
Urquhart, A. S., Vogan, A. A., Gardiner, D. M., & Idnurm, A. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2214521120 · Cited by 57
Metadata
- Authors
- Ye, Y., & Godzik, A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-09-27
- Volume
- 19
- Issue
- suppl_2
- Pages
- ii246-ii255
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2097642323
- Cited by
- 616
- References
- 21
- FWCI
- 3.00
- Type
- journal article
- Language
- en
- Open access
- closed
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