A Graph-theoretic Approach to the Identification of Three-dimensional Patterns of Amino Acid Side-chains in Protein Structures

Artymiuk, Peter J.; Poirrette, Andrew R.; Grindley, Helen M.; Rice, David W.; Willett, Peter

doi:10.1006/jmbi.1994.1657

Cited by 194 publications

(168 citation statements)

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“…Previous work has described the use of subgraph isomorphism algorithms for the rapid comparison of 3D protein structures [21,28]. Here, we describe the program NASSAM, in which a subgraph isomorphism algorithm is used to compare 3D nucleic acid structures at the base level.…”

Section: The Graph Representationmentioning

confidence: 99%

“…These secondary structure element searches were able to demonstrate similarities between protein families that had been previously unnoticed [26,27,17]. The techniques were then developed to search for 3D patterns of amino acid side chains contained in protein structures [28]. Graph-theoretic methods have also been used in detection of protein side chain clustering with the nodes and edges representing the C β atoms and distances between them respectively [29] and in pattern matching of binding pocket properties [30].…”

Section: Introductionmentioning

confidence: 99%

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Representation, searching and discovery of patterns of bases in complex RNA structures

Harrison

South

Willett

et al. 2003

Journal of Computer-Aided Molecular Design

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SummaryWe describe a graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation. Two vectors represent each nucleic acid base and the relative positions of bases with respect to one another are described in terms of distances between the defined start and end points of the vectors on each base. These points comprise the nodes and the distances the edges of a graph, and a pattern search can then be performed using a subgraph isomorphism algorithm.The minimal representation was designed to facilitate searches for complex patterns but was first tested on simple, well-characterised arrangements of bases such as base pairs and GNRA-tetraloop receptor interactions. The method performed very well for these interaction types. A survey of side-by-side base interactions, of which the adenosine platform is the best known example also locates examples of similar base rearrangements that we consider to be 2 important in structural regulation. A number of examples were found, with GU platforms being particularly prevalent. A GC platform in the RNA of the Thermus thermophilus small ribosomal subunit is in an analogous position to an adenosine platform in other species. An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA.Abbreviations PDB Protein Databank 3D three-dimensional GNRA Guanine, N = any base, R = pyrimidine base, Adenine 3

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Section: The Graph Representationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Representation, searching and discovery of patterns of bases in complex RNA structures

Harrison

South

Willett

et al. 2003

Journal of Computer-Aided Molecular Design

Self Cite

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“…As a direct comparison with the method by Artymiuk et al (1994Artymiuk et al ( , 1995, a motif was used composed of the zinc-binding side-chains of thermolysin (His142, His146, Glu166; PDB code 4TMN). Artymiuk et al (1994) found matches with zinc and iron-binding sites in ®ve distinct proteins, namely thermolysin itself, carboxypeptidase, haemoglobin, hemerythrin, and the photosynthetic reaction centre.…”

Section: Metal-binding Site Recognitionmentioning

confidence: 99%

“…However, macromolecules and macromolecular databases have been less amenable to similar analyses. A few years ago, Artymiuk et al (1994Artymiuk et al ( , 1995 described a program called ASSAM which could be used to query the PDB using motifs consisting of side-chains of amino acid residues. Internally, a motif was represented by the distance matrix between pseudo-atoms (1, 2, or 3 per side-chain), and database proteins were represented similarly, which enabled the use of subgraph-isomorphism algorithms to ®nd matches.…”

Section: Introductionmentioning

confidence: 99%

Recognition of spatial motifs in protein structures 1 1Edited by J. Thornton

Kleywegt

1999

Journal of Molecular Biology

291

240

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As the structural database continues to expand, new methods are required to analyse and compare protein structures. Whereas the recognition, comparison, and classi®cation of folds is now more or less a solved problem, tools for the study of constellations of small numbers of residues are few and far between. In this paper, two programs are described for the analysis of spatial motifs in protein structures. The ®rst, SPASM, can be used to ®nd the occurrence of a motif consisting of arbitrary main-chain and/or side-chains in a database of protein structures. The program also has a unique capability to carry out``fuzzy pattern matching'' with relaxed requirements on the types of some or all of the matching residues. The second program, RIGOR, scans a single protein structure for the occurrence of any of a set of pre-de®ned motifs from a database. In one application, spatial motif recognition combined with pro®le analysis enabled the assignment of the structural and functional class of an uncharacterised hypothetical protein in the sequence database. In another application, the occurrence of short left-handed helical segments in protein structures was investigated, and such segments were found to be fairly common. Potential applications of the techniques presented here lie in the analysis of (newly determined) structures, in comparative structural analysis, in the design and engineering of novel functional sites, and in the prediction of structure and function of uncharacterised proteins.

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“…Another example is given by the active site of enolase superfamily, which can be accurately characterized by the spatial arrangement of five residues. 4 A number of methods [5][6][7][8][9][10][11][12][13][14][15][16] were developed to identify this type of structural motif, taking advantage of the distance constraints of the conserved residues.…”

Section: Introductionmentioning

confidence: 99%

The fragment transformation method to detect the protein structural motifs

Lin

Chen

et al. 2006

Proteins

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To identify functional structural motifs from protein structures of unknown function becomes increasingly important in recent years due to the progress of the structural genomics initiatives. Although certain structural patterns such as the Asp-His-Ser catalytic triad are easy to detect because of their conserved residues and stringently constrained geometry, it is usually more challenging to detect a general structural motifs like, for example, the ␤␤␣-metal binding motif, which has a much more variable conformation and sequence. At present, the identification of these motifs usually relies on manual procedures based on different structure and sequence analysis tools. In this study, we develop a structural alignment algorithm combining both structural and sequence information to identify the local structure motifs. We applied our method to the following examples: the ␤␤␣-metal binding motif and the treble clef motif. The ␤␤␣-metal binding motif plays an important role in nonspecific DNA interactions and cleavage in host defense and apoptosis. The treble clef motif is a zinc-binding motif adaptable to diverse functions such as the binding of nucleic acid and hydrolysis of phosphodiester bonds. Our results are encouraging, indicating that we can effectively identify these structural motifs in an automatic fashion. Our method may provide a useful means for automatic functional annotation through detecting structural motifs associated with particular functions. Proteins 2006;63:636 -643.

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A Graph-theoretic Approach to the Identification of Three-dimensional Patterns of Amino Acid Side-chains in Protein Structures

Cited by 194 publications

References 0 publications

Representation, searching and discovery of patterns of bases in complex RNA structures

Representation, searching and discovery of patterns of bases in complex RNA structures

Recognition of spatial motifs in protein structures 1 1Edited by J. Thornton

The fragment transformation method to detect the protein structural motifs

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