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

....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.

....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

....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.

....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.

....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.

....feature of this set of proteins is that except for the similarities among the pairs there are no additional homologies among any two proteins. Also, the benchmark set represents the currently known fold classes. The distribution of secondary structure classes is similar to the one observed in PDB (Orengo et al. 1997). The relative frequencies are 27 (22 ) all ff, 30 (32 ) all fi, 42 (44 ) ff fi, and 0:6 (1:2 ) low secondary structure content, where the numbers in parentheses correspond to the average values in PDB. According to the CATH structure classification version 1.6 (Orengo et al. 1997) the pairs ....

....in PDB (Orengo et al. 1997) The relative frequencies are 27 (22 ) all ff, 30 (32 ) all fi, 42 (44 ) ff fi, and 0:6 (1:2 ) low secondary structure content, where the numbers in parentheses correspond to the average values in PDB. According to the CATH structure classification version 1. 6 (Orengo et al. 1997), the pairs correspond to 63 different topologies with all the 10 known superfolds represented. Correct alignments Assessment of alignment accuracy requires that the correct alignment for each pair is known. This in turn requires that the term correct alignment is defined in a suitable way. The ....

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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.

....define a motif present in different domains thereby specifying a finer level of granularity than previously described in a systematic way. Comparison of Common Substructures With scop Folds Consider a typical example. Four neighbors (1LDE:C, 2PIA: 1VPT: and 1BNC:A) containing substructure [9] (1AV6:A) clearly a Rossmann fold, are assigned to different folds by scop 6 (Table III) These four neighbors are similar to the master representative 1AV6:A with a rmsd ranging from 0.6 to 3.8. All four folds consist of parallel beta sheets with five or more strands and with alpha helices ....

....which are present in both common subdomains is given. The total number of neighbors in a given subdomain is provided in parenthesis. Subdomains are numbered as follows: 1]1TEN: 2]1RNL: 3]1A91: 4]1LDE:C, 5]1SMG: 6]1TIG: 7]1PDO: 8]1OFG:A, [9]1AV6:A, 10]1AUZ: 11]2PIA: 12]1VPT: 13]1IL7: 14]1BGD: 15]1OXP: 16]1BNC:A, 17]1ETU: 18]1APS: 19]1ECM:A, 20]1FDR: 21]1FCD:A, 22]1DNP:A, 23]1EFV:A, 24]256B:B, 25]1LBS: 26]1BRO:A, 27]1GOX: 28]1FFH: 29]2CHS:K, 30]1VSC:A, 31]2MNR: ....

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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.

....can define a motif present in different domains thereby specifying a finer level of granularity than previously described in a systematic way. Comparison of Common Substructures with scop Folds Consider a typical example. Four neighbors (1LDE:C, 2PIA: 1VPT: and 1BNC:A) containing substructure [9] (1AV6:A) clearly a Rossmann fold, are assigned to different folds by scop 6 (Table III) These four neighbors are similar to the master representative 1AV6:A with an rmsd ranging from 0.6 to 3.8 o A . All four folds consist of parallel beta sheets with 5 or more strands and with alpha ....

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 5:1093-1108, 1997.

.... efficient query processing algorithms are available even for high dimensional histograms [Sei 97] 5 Experimental Evaluation For our experiments, we used the example protein 1SER B from above, a Seryl tRNA Synthetase molecule from the PDB [Ber 77] From the protein classification system CATH [Ore 97] we obtained information on structurally similar molecules, and found the family of Seryl tRNA Synthetases which we illustrate in figure 4. Obviously, from a visual inspection, the strong shape similarity of the molecules can be observed. 0 100 200 300 400 500 ALA ASN CYS GLU HIS LEU MET ....

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, No. 8, 1997, pp 1093-1108.

....substructures of the molecules such as alpha helices or beta sheets. The evaluation of a pair of proteins is very expensive, and query processing for a single molecule against the entire database currently takes an overnight run on a workstation. Another classification schema is provided by CATH [OMJ 97] a hierarchical classification of protein domain structures, which clusters proteins at four major levels, class (C) architecture (A) topology (T) and homologous superfamily (H) The class label is derived from secondary structure content and cannot be assigned for all protein structures ....

....[Kas 98] 4.1 Basic Similarity Search In order to illustrate the applicability of the similarity model, we demonstrate the retrieval of the members of a known family. As a typical example, we chose the seven SeryltRNA Synthetase molecules from our database that are classified by CATH [OMJ 97] to the same family. The diagram in Figure 7 presents the result using shape histograms for 6 shells and 20 sectors. The seven members of the Seryl family rank on the top seven positions among the 5,000 molecules of the database. In particular, the similarity distance noticeable increases for ....

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, No. 8 (1997) 1093-1108

....structure were removed from the set. From the resulting set al..l chains with non compact structure, transmembrane proteins and virus capsid proteins were also eliminated. All structures of the final data set were split into domains according to information from SCOP (Murzin et al. 1995) CATH (Orengo et al. 1997) or publications of the experimentalists (Table 1) Structure comparison All structure comparisons were performed with the program ProSup which implements rigid body superimposition of two proteins (Feng Sippl, 1996) Parameters were set as described by Lackner et al. 1999) ProSup measures ....

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.

....structures is rapidly increasing and more than 9000 complete sets of coordinates were available at the end of 1998. Many research groups maintain web accessible databases of protein folds, which divide the conformational space into structural hierarchies (nested groups) e.g. FSSP [7] CATH [8], SCOP [9] MMDB [10] and 3Dee [11] Each group has its own way to compare and classify proteins. Here we consider two such databases, the FSSP database created by Holm and Sander [12,13] and the CATH database created by Orengo et al. 8] The FSSP database The FSSP (Fold classification based on ....

....structural hierarchies (nested groups) e.g. FSSP [7] CATH [8] SCOP [9] MMDB [10] and 3Dee [11] Each group has its own way to compare and classify proteins. Here we consider two such databases, the FSSP database created by Holm and Sander [12,13] and the CATH database created by Orengo et al. [8]. The FSSP database The FSSP (Fold classification based on Structure Structure alignment of Proteins) uses a fully automated structure comparison algorithm, DALI (Distances ALIgnment algorithm) 7] to calculate a pairwise structural similarity measure (the S score) between protein chains. The ....

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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.

.... than 8000 three dimensional strcutures available in the public repository maintained by the Brookhaven National Laboratory (Bernstein et al. 1977) To facilitate understanding of protein structure classification shemes have been developed; the main schemes are Scop (Brenner et al. 1996) and Cath (Orengo et al. 1997). In Scop the basic unit is a domain, a structure or substructure that is considered to be folded independently. Small proteins have a single domain, for larger ones, a domain is a substructure, indicated by a chain id and or a sequence interval range. Domains are grouped into families. Domains of ....

Orengo, C., Michie, A., Jones, S., Jones, D., Swindells, M., and Thornton, J. (1997). CATH -- a hierarchic classification of protein domain structures.

....between structure and function, and for more accurate predictions on the functional role of proteins. Structure based analyses are not discussed in this thesis. For studies which are focused on classification of known protein structures into structural classes see [Orengo 1994, Murzin et al. 1995, Orengo et al. 1997] It should be noted that structure comparison algorithms are mostly heuristics, and are usually very computationally intensive. Moreover, an expert knowledge is usually needed to obtain accurate 1 This method projects the sequence space onto an two dimensional Euclidean space, so that the ....

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.

....1 . The data set should be useful on its own. Prolog has already proven to be an excellent tool to manage protein structure databases [13, 14] 3.1 Structure Classification The classification of protein structures is a complex task. The main classification schemes are SCOP [12] and CATH [15]. The former classification is performed manually while the second is semi automated. For this work we refer to SCOP, it is used to relate structures and folds. 1 See http: www.icnet.uk bmm people turcotte ilp98 The basic unit in SCOP is a domain, a structure or substructure that is ....

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.

....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.

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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

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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.

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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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Orengo CA, Michie AD, Jones S, Swindells MB, Thornton JM. CATH---a hierarchic classification of protein domain structures. Structure 1997;5:1093--1108. The CATH database is available on-line at http://www.biochem.ucl.ac.uk/bsm/cath/

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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 5:1093--1108, 1997. 532 M. GERSTEIN

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