CATH--a hierarchic classification of protein domain structures. Export

@article{citeulike:226925, abstract = {BACKGROUND: Protein evolution gives rise to families of structurally related proteins, within which sequence identities can be extremely low. As a result, structure-based classifications can be effective at identifying unanticipated relationships in known structures and in optimal cases function can also be assigned. The ever increasing number of known protein structures is too large to classify all proteins manually, therefore, automatic methods are needed for fast evaluation of protein structures. RESULTS: We present a semi-automatic procedure for deriving a novel hierarchical classification of protein domain structures (CATH). The four main levels of our classification are protein class (C), architecture (A), topology (T) and homologous superfamily (H). Class is the simplest level, and it essentially describes the secondary structure composition of each domain. In contrast, architecture summarises the shape revealed by the orientations of the secondary structure units, such as barrels and sandwiches. At the topology level, sequential connectivity is considered, such that members of the same architecture might have quite different topologies. When structures belonging to the same T-level have suitably high similarities combined with similar functions, the proteins are assumed to be evolutionarily related and put into the same homologous superfamily. CONCLUSIONS: Analysis of the structural families generated by CATH reveals the prominent features of protein structure space. We find that nearly a third of the homologous superfamilies (H-levels) belong to ten major T-levels, which we call superfolds, and furthermore that nearly two-thirds of these H-levels cluster into nine simple architectures. A database of well-characterised protein structure families, such as CATH, will facilitate the assignment of structure-function/evolution relationships to both known and newly determined protein structures.}, address = {Department of Biochemistry and Molecular Biology, University College London, UK.}, author = {Orengo, C. A. and Michie, A. D. and Jones, S. and Jones, D. T. and Swindells, M. B. and Thornton, J. M.}, citeulike-article-id = {226925}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/9309224}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=9309224}, day = {15}, issn = {0969-2126}, journal = {Structure (London, England : 1993)}, keywords = {cath, fold\_classification}, month = {August}, number = {8}, pages = {1093--1108}, posted-at = {2008-07-30 08:17:48}, priority = {2}, title = {CATH--a hierarchic classification of protein domain structures.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/9309224}, volume = {5}, year = {1997} }

TY - JOUR ID - citeulike:226925 L3 - citeulike-article-id:226925 N2 - BACKGROUND: Protein evolution gives rise to families of structurally related proteins, within which sequence identities can be extremely low. As a result, structure-based classifications can be effective at identifying unanticipated relationships in known structures and in optimal cases function can also be assigned. The ever increasing number of known protein structures is too large to classify all proteins manually, therefore, automatic methods are needed for fast evaluation of protein structures. RESULTS: We present a semi-automatic procedure for deriving a novel hierarchical classification of protein domain structures (CATH). The four main levels of our classification are protein class (C), architecture (A), topology (T) and homologous superfamily (H). Class is the simplest level, and it essentially describes the secondary structure composition of each domain. In contrast, architecture summarises the shape revealed by the orientations of the secondary structure units, such as barrels and sandwiches. At the topology level, sequential connectivity is considered, such that members of the same architecture might have quite different topologies. When structures belonging to the same T-level have suitably high similarities combined with similar functions, the proteins are assumed to be evolutionarily related and put into the same homologous superfamily. CONCLUSIONS: Analysis of the structural families generated by CATH reveals the prominent features of protein structure space. We find that nearly a third of the homologous superfamilies (H-levels) belong to ten major T-levels, which we call superfolds, and furthermore that nearly two-thirds of these H-levels cluster into nine simple architectures. A database of well-characterised protein structure families, such as CATH, will facilitate the assignment of structure-function/evolution relationships to both known and newly determined protein structures. IS - 8 JF - Structure (London, England : 1993) SN - 0969-2126 AD - Department of Biochemistry and Molecular Biology, University College London, UK. EP - 1108 TI - CATH--a hierarchic classification of protein domain structures. VL - 5 SP - 1093 KW - cath KW - fold_classification AU - Orengo, CA AU - Michie, AD AU - Jones, S AU - Jones, DT AU - Swindells, MB AU - Thornton, JM PY - 1997/08/15/ UR - http://view.ncbi.nlm.nih.gov/pubmed/9309224 ER -