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Wallace AC, Borkakorti N, Thornton JM: TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases: Application to enzyme active-sites. Protein Sci 1997, 6:2308-2323. This paper presents a geometric hashing approach to searching for a predefined cluster of residues. The dataset of PDB entry files is preprocessed to create a file for each 'reference' amino acid sidechain, for example, the five-member histidine ring. These files are large, but can be searched very rapidly for hits against a defined template. The authors extend their previous work on the catalytic Ser-His-Asp triad [45] to explore several other functional sites. A preliminary database of 3D templates for a few active sites is also presented - PROCAT (http://www.biochem.ucl.ac.uk/bsm/).
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Protein Sci
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Wallace, A.C.1
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Three-dimensional structure analysis of PROSITE patterns
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Kasuya A, Thornton JM: Three-dimensional structure analysis of PROSITE patterns. J Mol Biol 1999, 286:1673-1691. This paper addresses the problem of finding automated approaches for defining 3D templates for functional sites. The PDB is searched for matches to the PROSITE motif sequence library. Hits for the 20 most common motifs are then analysed to explore whether the sequence motifs adopt the same conformation in each hit. The data presented support the hypothesis that the coordinate data can discriminate between true and false hits. Thus, the 3D templates derived from PROSITE may provide a useful source of structural motifs for functional sites; however, an extension from the Cα template will be needed to identify recurrent sidechain motifs that occur on different frameworks.
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Kasuya, A.1
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Discovery of local packing motifs in protein structures
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Jonassen I, Eidhammer I, Taylor WR: Discovery of local packing motifs in protein structures. Proteins 1999, 34:206-219. A fast, pattern-matching method is described for identifying local packing motifs. The spatial neighbourhood of each residue is described as a string, allowing sequence pattern search methods to find patterns that are common to subsets of the strings. There are restrictions on the spatial position of each residue, the order along the chain and residue identity. Patterns identified were checked for spatially similar substructures. The method was tested on four different protein families - serine proteases, cupredoxins, cysteine proteinases and ferredoxins - and identified structural motifs that corresponded well with the known site information for these proteins. As a result of the constraints used, the method will be of most use in identifying common sites in homologous proteins.
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Proteins
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Jonassen, I.1
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Taylor, W.R.3
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Karlin S, Zhu Z-Y: Characterizations of diverse residue clusters in protein three-dimensional structures. Proc Natl Acad Sci USA 1996, 93:8344-8349.
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Karlin S, Zhu Z-Y: Clusters of charged residues in protein three-dimensional structures. Proc Natl Acad Sci USA 1996, 93:8350-8355.
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A method to search for similar protein local structures at ligand-binding sites and its application to adenine recognition
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Kobayashi N, Go N: A method to search for similar protein local structures at ligand-binding sites and its application to adenine recognition. Eur Biophys J 1997, 26:135-144. The geometrical properties of protein active sites were captured using Delaunay tessellation to define the space near a given chemical moiety. All heavy atoms, including water, were considered in the selection of surrounding atoms. In order to compare similar sites in a pair of proteins, these spatial arrangements are translated and rotated so that the chemical moieties are superposed on each other. The method is not constrained by the sequentiality of the polypeptide chain and has been applied to identifying modes of nucleotide base recognition by proteins (see [52]).
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Eur Biophys J
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ATP-binding proteins with different folds share a common ATP-binding structural motif
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Kobayashi N, Go N: ATP-binding proteins with different folds share a common ATP-binding structural motif. Nat Struct Biol 1997, 4:6-7.
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Two 'unrelated' families of ATP-dependent enzymes share extensive structural similarities about their cofactor binding sites
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Denessiouk KA, Lehtonen JV, Korpela T, Johnson MS: Two 'unrelated' families of ATP-dependent enzymes share extensive structural similarities about their cofactor binding sites. Protein Sci 1998, 7:1136-1146.
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Structural motif of phosphate-binding site common to various protein superfamilies: All-against-all structural comparison of protein-mononucleotide complexes
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Kinoshita K, Sadanami K, Kidera A, Go N: Structural motif of phosphate-binding site common to various protein superfamilies: All-against-all structural comparison of protein-mononucleotide complexes. Protein Eng 1999, 12:11-14.
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Identification of protein three-dimensional side-chain patterns: New examples of convergent evolution
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Russell RB: Identification of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol 1998, 279:1211-1227. This paper presents a new automated method for detecting recurring three-dimensional sidechain patterns in protein structures without any prior knowledge of the active site or binding site residues. A depth-first search algorithm detects all spatially adjacent groups of identical amino acids that are common to two proteins. The vast number of combinations is reduced by using knowledge derived from multiple sequence alignments to concentrate on conserved polar residues (i.e. those that are likely to be involved in functional sites). The statistical significance of any fit was assessed using a 'theoretical' distribution fitted to simulated data. The power of the method is illustrated using known examples (e.g. the His-Ser-Asp catalytic triad). More interestingly, an all-against-all comparison of known structures reveals several new examples of common sidechain patterns within different folds. This excellent paper facilitates the recognition of active sites from structures and sequence alignments.
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J Mol Biol
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Russell, R.B.1
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Rosen M, Lin SL, Wolfson H, Nussinov R: Molecular shape comparisons in searches for active sites and functional similarity. Protein Eng 1998, 11:263-277.
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Jones S, Thornton JM: Analysis of protein-protein interaction sites using surface patches. J Mol Biol 1997, 272:121-132.
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Freedman RB: Novel disulphide oxidoreductase in search of a function. Nat Struct Biol 1998, 5:531-532.
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