Cited by 3,984Protein Structure and DynamicsEnzyme Structure and FunctionGenomics and Phylogenetic Studies

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Protein Structure Comparison by Alignment of Distance Matrices

Holm, Liisa, Sander, Chris·1993·Journal of Molecular Biology

DOI 10.1006/jmbi.1993.1489

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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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Method
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Cheung, J., & Hendrickson, W. A. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m805253200 · Cited by 112
The Structure of the RlmB 23S rRNA Methyltransferase Reveals a New Methyltransferase Fold with a Unique Knot
Michel, G., Sauvé, V., Larocque, R., et al. (2002) · Structure · doi:10.1016/s0969-2126(02)00852-3 · Cited by 112
Structure and Function of the C-terminal Domain of the Polymerase Cofactor of Rabies Virus
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Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 å resolution
Peat, T. S., Newman, J. M., Waldo, G. S., Berendzen, J., & Terwilliger, T. C. (1998) · Structure · doi:10.1016/s0969-2126(98)00120-8 · Cited by 112
Crystal Structure of the Vesicular Transport Protein Sec17
Rice, L. M., & Brünger, A. T. (1999) · Molecular Cell · doi:10.1016/s1097-2765(00)80190-2 · Cited by 112
“Comparison to Tetratricopeptide Repeats Despite the local structural similarity of the Sec17 repeats to TPRs, the overall twist of the sheet of a helicesThree-dimensional alignment using DALI (Holm and Sander, 1993) of the Sec17 structure against a represen- in Sec17 differs significantly from that of PP5 (Figure 5).”
Background
Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress‐related protein
Singh, S., Cornilescu, C. C., Tyler, R. C., Cornilescu, G., Tonelli, M., Lee, M. S., & Markley, J. L. (2005) · Protein Science · doi:10.1110/ps.051579205 · Cited by 112
“Structural homologs identified by the DALI server (Holm and Sander 1993) had minimal sequence identity (4%–6%) with At1g01470.”
Background
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure
Lewis, D. P., Jebara, T., & Noble, W. S. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl475 · Cited by 110
Practical limits of function prediction
Devos, D. P., & Valencia, A. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20001001)41:1 · Cited by 358
A protein taxonomy based on secondary structure.
Rose, G. D., Przytycka, T. M., & Aurora, R. (1999) · Nature Structural Biology · doi:10.1038/10728 · Cited by 112
Crystal structure of Rab geranylgeranyltransferase at 2.0 Å resolution
Zhang, H., Seabra, M. C., & Deisenhofer, J. (2000) · Structure · doi:10.1016/s0969-2126(00)00102-7 · Cited by 111
Structural Insight into the Dual Ligand Specificity and Mode of High Density Lipoprotein Association of Apolipoprotein D
Eichinger, A., Nasreen, A., Kim, H. J., & Skerra, A. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m703552200 · Cited by 111
A Structural and Functional Analysis of α-Glucan Recognition by Family 25 and 26 Carbohydrate-binding Modules Reveals a Conserved Mode of Starch Recognition
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Crystal Structure of Neisserial Surface Protein A (NspA), a Conserved Outer Membrane Protein with Vaccine Potential
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Structure of a Heterotetrameric Geranyl Pyrophosphate Synthase from Mint ( Mentha piperita ) Reveals Intersubunit Regulation
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“, 2006), two homodimeric PTSs having the highest DALI scores, (highest structural similarities) toMpGPPS, and the regions corresponding to AC loop 1 showed dramatic ligand binding-induced conformational changes necessary for substrate entry or product release (Holm and Sander, 1993) (see Supplemental Figure 10 online).”
Background
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures
Redfern, O., Harrison, A., Dallman, T. J., Pearl, F. M. G., & Orengo, C. A. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030232 · Cited by 106
“CATHEDRAL and DDP (a modiﬁed version of the SSAP algorithm [27]) were benchmarked against other publicly available structural comparison methods, STRUCTAL [29], DALI [26], LSQMAN, and CE [30] (see Text S1 for description of methods).”
BackgroundMethod
The 1.6-Å crystal structure of the class of chaperones represented by Escherichia coli Hsp31 reveals a putative catalytic triad
Quigley, P. M., Korotkov, K. V., Baneyx, F., & Hol, W. G. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0530312100 · Cited by 109
Three-Dimensional Solution Structure of Oryzacystatin-I, a Cysteine Proteinase Inhibitor of the Rice, Oryza sativa L. japonica,
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Solution structure of the origin DNA-binding domain of SV40 T-antigen
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Heme packing motifs revealed by the crystal structure of the tetra-heme cytochrome c554 from Nitrosomonas europaea
Iverson, T. M., Arciero, D. M., Hsu, B. T., et al. (1998) · Nature Structural Biology · doi:10.1038/2975 · Cited by 110
“A search of the Brookhaven Protein Data bank using the EMBL Dali serve”
FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately
Budowski-Tal, I., Nov, Y., & Kolodny, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914097107 · Cited by 111
“The gold-standard answer includes neighbors found by a best-of-six structural aligner (using SSAP (26), STRUCTAL, DALI (27), LSQMAN (28), CE, and SSM); this expensive computation was done previously (10).”
Method
Structure of the C-terminal domain of FliG, a component of the rotor in the bacterial flagellar motor
Lloyd, S. A., Whitby, F. G., Blair, D. F., et al. (1999) · Nature · doi:10.1038/22794 · Cited by 109

Authors: Holm, L., & Sander, C.
Affiliations: European Molecular Biology Laboratory (DE)
ORCID: Holm, Liisa
Sander, Chris
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 1993-09
Volume: 233
Issue: 1
Pages: 123-138
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1006/jmbi.1993.1489
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
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
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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Protein Structure Comparison by Alignment of Distance Matrices

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