Orengo, C., Michie, A., Jones, S., Jones, D., Swindells, M., Thornton, J.: CATH--a hierarchic classification of protein domain structures. Structure. 5 (1997) 1093--108 Home/Search Document Not in Database Summary Related Articles Check |
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Bootstrapping and Normalization for Enhanced Evaluations of.. - Green, Brenner (2002) (1 citation) (Correct)
....structure evolves more slowly than sequence, structural similarity can be used as a gold standard for determining whether any two sequences are related. To this end, analyses frequently use the classifications in the Structural Classification of Proteins (SCOP) 5] 6] 35] 37] and CATH [38] [40] databases, as well as direct structural similarity [41] The SCOP database provides a hierarchical classification of the structural domains of all solved protein structures. Domains are classified at the level of class, fold, superfamily, and family. ASTRAL [4] provides sequence sets of ....
C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton, "CATH---A hierarchic classification of protein domain structures," Structure, vol. 5, pp. 1093--1108, 1997.
Analysis of Secondary Structure Elements of Proteins.. - Guerra, Lonardi, Zanotti (2002) (Correct)
....this paper we consider the problem of matching a query protein against a database of existing proteins for the automatic assignment of a newly determined structure to one of the existing protein families. This is a problem that has recently received a lot of attention in the biological literature [19, 20]. We propose an approach to solve this problem based on indexing using geometric invariants of the secondary structures of the proteins. We consider all triplets of secondary structures and their associated best fit linear segments. Geometric properties of the three linear segments are computed ....
Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M. (1997). CATH- A Hierarchic Classification of Protein Domain Structures. Structure, 5, 1093-1108
Pattern Matching and Pattern Discovery Algorithms for Protein.. - Gilbert (2001) (Correct)
....is to find hypotheses about its function. One possible approach is pairwise comparison of the structure with the structures of proteins whose functions are already known. There are already several tools that allow such comparisons, for example DALI [7] http: www.ebi.ac. uk dali ) or CATH [11] (http: www.biochem.ucl.ac.uk bsm cath ) However there are two weaknesses with such approach. Firstly, as the number of proteins with given structure is growing the time needed to do such comparisons is also growing. Currently there are about 15000 protein structure descriptions deposited in the ....
....i.e. what is the probability that the fact that a protein matches a given motif implies that protein has also some real similarity with other proteins characterised by the same motif. To do this, we have tried to compare our approach against the existing CATH protein classification database. CATH [11] is a hierarchical classification of protein domain structures, which clusters proteins at four major levels Class (C) Architecture (A) Topology (T) and Homologous superfamily (H) There are four different C classes mainly alpha (class 1) mainly beta (class 2) alphabeta (class 3) and low ....
Orengo, C.A., Michie, A.D., Jones, S., Swindelis, M.B.: CATH -- a hierarchic classification of protein domain structures. Structure 5 (1997) 1093--1108.
Comparing Genomes in terms of Protein Structure: Surveys of a .. - Gerstein, Hegyi (1998) (2 citations) (Correct)
....progress being made in genomics, there is a tremendous investment being made in structural biology. This is yielding great returns in the form of an exponentially increasing number of protein structures. All these structures fall into a very limited number of folding patterns, currently about 350 [6 10]. It is believed, furthermore, that we will eventually find that all naturally occurring protein structures are composed of very small number of folds, estimated to be 1000 [11] The objective of this work is to discuss various means of understanding this finite universe of genes in terms of an ....
.... the approach taken for the scop classification of protein structures [7] On another extreme, there are a number of algorithms for automatically comparing structures and clustering them into fold families [76 89] Finally, there is a hybrid approach, based on both automatic and manual comparison [10, 90]. Completely automatic methods have the advantage of speed and objectivity. However, the fold classifications produced by a computer are not always as understandable or reliable as those produced by humans. Furthermore, although manual classification is slow, if it is done correctly, it only has ....
Orengo, C A, Michie, A D, Jones, S, Jones, D T, Swindells, M B & Thornton, J M (1997) CATH--a hierarchic classification of protein domain structures. Structure 5, 1093-1108.
On Hydrophobicity Correlations in Protein Chains - Irbäck, Sandelin (2000) (Correct)
....et al. 1995) This choice makes it possible for us to improve significantly on the statistics in the previous study (Irback et al. 1997) which was based on an off lattice model. The real sequences studied are single domain enzymes taken from the CATH protein structure classification database (Orengo et al. 1997), which we hope displays statistical properties representative of functional (globular) folding units. With this restriction on protein type, it turns out that the previous, somewhat artificial, restriction on total hydrophobicity (Irback et al. 1996) can be lifted. 2 2 Methods 2.1 Sequences ....
....somewhat artificial, restriction on total hydrophobicity (Irback et al. 1996) can be lifted. 2 2 Methods 2.1 Sequences Let us first define the sequences studied. The real sequences studied are the 173 nonhomologous single domain enzymes found in the October 1998 release of the CATH database (Orengo et al. 1997). These sequences are transformed into binary hydrophobicity strings, by taking the six amino acids Leu, Ile, Val, Phe, Met, and Trp as hydrophobic (oe i = 1) and the others as hydrophilic (oe i = Gamma1) This choice is somewhat arbitrary. Therefore, we also tried a 20 valued hydrophobicity ....
Orengo, C.A., A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells and J.M. Thornton. 1997. CATH --- A Hierarchic Classification of Protein Domain Structures. Structure. 5:1093--1108.
Genome Analysis: Assigning Protein Coding Regions to.. - Salamov, Suwa.. (1999) (2 citations) Self-citation (Orengo Swindells) (Correct)
....that can be identified on the basis of sequence analysis alone because these always precede the use of slower fold recognition. Furthermore we want to provide a method that can be immediately applied to all finished genomes. Our work takes advantage of several developments: 1) CATH database [6]: which classifies homologues on the basis of structural and functional similarities. 2) The benefits of using intermediate sequences [2, 7] in sequence searching. 3) PSI blast: the automated iterative search techniques [1] which allows more sensitive searches. This work describes an automated ....
Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M., CATH-- a hierarchic classification of protein domain structures, Structure, 5:1093-1108, 1997.
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Orengo, C., Michie, A., Jones, S., Jones, D., Swindells, M., Thornton, J.: CATH--a hierarchic classification of protein domain structures. Structure. 5 (1997) 1093--108
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C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. Cath -- a hierarchic classification of protein domain structures. Structure, 5(8):1093-- 1108, 1997.
Domain Discovery Method for Topological Profile Searches .. - Viksna, Gilbert.. (2004) (Correct)
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Orengo, C.A., Michie, A.D., Jones, S., and Swindelis, M.B., CATH - a hierarchic classification of protein domain structures, Structure 5:1093--1108, 1997.
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C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thorton. CATH- a hierarchic classification of protein domain structures. Structure, 5(8):1093--1108, 1997.
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Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M., CATH - a hierarchic classification of protein domain structures, Structure, 5:1093--1108, 1997.
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Orengo, C., Michie, A., Jones, S., Jones, D., Swindells, M. & Thornton, J. (1997). CATH---a hierarchic classification of protein domain structures. Structure, 5, 1093 -- 1108.
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C.A. Orengo, A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton. CATH-a hierarchic classification of protein domain structures. Structure, 5:1093--1108, 1997.
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Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., Thornton, J.M.: CATH- A Hierarchic Classification of Protein Domain Structures. Structure, Vol. 5(8) (1997) 1093-1108
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C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. CATH---a hierarchic classification of protein domain structures. Structure, 5(8):1093--1108, 1997.
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C.A. Orengo, A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton. CATH - a hierarchic classification of protein domain structures. Structure, 5:1093-1108, 1997.
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C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. Cath--a hierarchic classification of protein domain structures. Structure, 5(8):1093--108, 1997. 97454794 0969-2126 Journal Article.
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C.A. Orengo, A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton. CATH: a hierarchic classification of protein domain structures Structure, 5:10931108, 1997. 11
Prediction of Contact Maps Using Support Vector Machines - Zhao, Karypis (2003) (3 citations) (Correct)
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C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. CATH---a hierarchic classification of protein domain structures. Structure, 5(8):1093--1108, 1997.
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Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, and Thornton JM. CATH - a hierarchic classification of protein domain structures . Structure 1997; 5:1093--1108.
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Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH: A hierarchic classification of protein domain structures. Structure 1997; 5: 10931108.
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Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH---a hierarchic classification of protein domain structures. Structure 1997;5:1093--1108.
Large-Scale Comparison of Protein Sequence Alignment.. - Sauder, Arthur, Dunbrack (2000) (5 citations) (Correct)
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Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton J. CATH---a hierarchic classification of protein domain structures. Structure 1997;5:1093--1108.
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Orengo,C.A., Michie,A.D., Jones,S., Jones,D.T., Swindells,M.B. and Thornton,J.M. (1997) CATH---a hierarchic classification of protein domain structures. Structure, 8, 1093--1108.
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Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH---a hierarchic classification of protein domain structures. Structure 1997;5:1093 --1108.
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