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Protein Structure Comparison by Alignment of Distance Matrices
Abstract
With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residue-residue (C alpha-C alpha) distance matrices. The distance matrices are first decomposed into elementary contact patterns, e.g. hexapeptide-hexapeptide submatrices. Then, similar contact patterns in the two matrices are paired and combined into larger consistent sets of pairs. A Monte Carlo procedure is used to optimize a similarity score defined in terms of equivalent intramolecular distances. Several alignments are optimized in parallel, leading to simultaneous detection of the best, second-best and so on solutions. The method allows sequence gaps of any length, reversal of chain direction and free topological connectivity of aligned segments. Sequential connectivity can be imposed as an option. The method is fully automatic and identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions. An all-against-all alignment of over 200 representative protein structures results in an objective classification of known three-dimensional folds in agreement with visual classifications. Unexpected topological similarities of biological interest have been detected, e.g. between the bacterial toxin colicin A and globins, and between the eukaryotic POU-specific DNA-binding domain and the bacterial lambda repressor.
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“The templates were pairwise structurally aligned according to DALILite (41,42), using HIF-2 α as a reference. The sequence alignments were obtained by CLUSTALW (43), and the result was confirmed using the Align-2D command within the MODELLER program (37-39).”
From Structural and Functional Characterization of the Aryl Hydrocarbon Receptor Ligand Binding Domain by Homology Modeling and Mutational Analysis (2007) · cites this paper as [41]
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Items 1,001–1,012 of 1,012
Senkovich, O., Cook, W. J., Mirza, S., Hollingshead, S. K., Protasevich, I. I., Briles, D. E., & Chattopadhyay, D. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.04.075 · Cited by 80
Pio, F., Kodandapani, R., Ni, C.-Z., Shepard, W., Klemsz, M., McKercher, S. R., Maki, R. A., & Ely, K. R. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.38.23329 · Cited by 81
Structure of the streptococcal cell wall C5a peptidase.
Brown, C. K., Gu, Z.-Y., Matsuka, Y. V., Purushothaman, S. S., Winter, L. A., Cleary, P. P., Olmsted, S. B., Ohlendorf, D. H., & Earhart, C. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504954102 · Cited by 70
Redundancy-Aware Topic Modeling for Patient Record Notes
Cohen, R., Aviram, I., Elhadad, M., & Elhadad, N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087555 · Cited by 71
“While in many natural language processing applications, redundancy is considered useful and its presence in a document collection is leveraged [24], in bioinformatics, for instance, it is standard practice to remove redundant sequences from databases [25] or to adjust for such sequences when using Gibbs sampling [26].”
BackgroundFraccalvieri, D., Soshilov, A. A., Karchner, S. I., Franks, D. G., Pandini, A., Bonati, L., Hahn, M. E., & Denison, M. S. (2013) · Biochemistry · doi:10.1021/bi301457f · Cited by 65
Mechanism of metal ion activation of the diphtheria toxin repressor DtxR
D'Aquino, J. A., Tetenbaum-Novatt, J., White, A., Berkovitch, F., & Ringe, D. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0500908102 · Cited by 57
1.2 Å crystal structure of the S. pneumoniae PhtA histidine triad domain a novel zinc binding fold
Riboldi-Tunnicliffe, A., Isaacs, N. W., & Mitchell, T. J. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.08.066 · Cited by 49
“used as search models gave a number of solutions in DALI [34] in which the overall fold (3 strands and an alpha helix) is preserved.”
MethodInfluentialBrigé, A., Leys, D., Meyer, T. E., Cusanovich, M. A., & Van Beeumen, J. J. (2002) · Biochemistry · doi:10.1021/bi012144b · Cited by 47
Crystal Structure of the Functional Unit of Interphotoreceptor Retinoid Binding Protein
Loew, A., & Gonzalez-Fernandez, F. (2002) · Structure · doi:10.1016/s0969-2126(01)00698-0 · Cited by 44
Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5
Lemak, A., Yee, A., Wu, H., Yap, D., Zeng, H., Dombrovski, L., Houliston, S., Aparicio, S., & Arrowsmith, C. H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077020 · Cited by 36
“To determine structural homologs of the PHD domain of MLL5 we used the DALI server [31].”
MethodCrystal structure of the MAP kinase binding domain and the catalytic domain of human MKP5
Tao, X., & Tong, L. (2007) · Protein Science · doi:10.1110/ps.062712807 · Cited by 31
“In addition, our structure is essentially identical to that reported recently for this domain (Jeong et al. 2006), with RMSD of ;0.37 Å between 145 equivalent Ca atoms.”
BackgroundResultInfluentialVaradi, M., Bordin, N., Orengo, C., & Velankar, S. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102543 · Cited by 29
Metadata
- Authors
- Holm, L., & Sander, C.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1993-09
- Volume
- 233
- Issue
- 1
- Pages
- 123-138
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2022058405
- Cited by
- 3,984
- References
- 0
- Citations by year
- 2026: 23 · 2025: 31 · 2024: 22 · 2023: 22 · 2022: 28 · 2021: 27 · 2020: 53 · 2019: 50 · 2018: 45 · 2017: 42 · 2016: 53 · 2015: 65 · 2014: 73 · 2013: 106 · 2012: 98
- FWCI
- 15.32
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- protein structure comparison, Dali, Monte Carlo optimization, structural similarity, protein fold classification, structural core, colicin A, globin, lambda repressor, sequence gaps
- MeSH terms
- Actins, Algorithms, Amino Acid Sequence, Colicins, DNA-Binding Proteins, Globins, Heat-Shock Proteins, Hexokinase, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Muramidase, Software, Reproducibility of Results, Cluster Analysis, Sequence Alignment, Sequence Homology, Amino Acid, Protein Structure, Secondary, Protein Structure, Tertiary
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