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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OpenStructure: an integrated software framework for computational structural biology
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The structural basis of the catalytic mechanism and regulation of glucose‐1‐phosphate thymidylyltransferase (RmlA)
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Solution structure of ShK toxin, a novel potassium channel inhibitor from a sea anemone
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Method
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Method
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Background
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Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1
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Structure of a presenilin family intramembrane aspartate protease
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An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3
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Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29
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Large-scale filament formation inhibits the activity of CTP synthetase
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“A similar evolutionary path could explain the structural similarity between hexokinase enzymes and the actin family of cytoskeletal elements (Holm and Sander, 1993; van den Ent et al., 2001).”
Ligand Preference Inferred from the Structure of Neutrophil Gelatinase Associated Lipocalin
Goetz, D. H., Willie, S. T., Armen, R. S., Bratt, T., Borregaard, N., & Strong, R. K. (2000) · Biochemistry · doi:10.1021/bi992215v · Cited by 184

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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