C A Orengo

Summary

Affiliation: University College London
Country: UK

Publications

  1. ncbi request reprint Classifying a protein in the CATH database of domain structures
    C A Orengo
    Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, Gower St, London WC1E 6BT, England
    Acta Crystallogr D Biol Crystallogr 54:1155-67. 1998
  2. ncbi request reprint Protein families and their evolution-a structural perspective
    Christine A Orengo
    Department of Biochemistry and Molecular Biology, University College, London WC1E 6BT, United Kingdom
    Annu Rev Biochem 74:867-900. 2005
  3. pmc The CATH Database provides insights into protein structure/function relationships
    C A Orengo
    Department of Biochemistry and Molecular Biology, Darwin Building, Univeristy College London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 27:275-9. 1999
  4. ncbi request reprint The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues
    J E Bray
    Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
    Protein Eng 13:153-65. 2000
  5. pmc A rapid classification protocol for the CATH Domain Database to support structural genomics
    F M Pearl
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 29:223-7. 2001
  6. ncbi request reprint Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction
    C A Orengo
    Department of Biochemistry and Molecular Biology, University College, London, United Kingdom
    Proteins . 1999
  7. pmc CORA--topological fingerprints for protein structural families
    C A Orengo
    Department of Biochemistry and Molecular Biology, University College, London, United Kingdom
    Protein Sci 8:699-715. 1999
  8. pmc Assigning genomic sequences to CATH
    F M Pearl
    Department of Biochemistry, University College London, University of London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 28:277-82. 2000
  9. ncbi request reprint From protein structure to function
    C A Orengo
    Biomolecular Structure and Modelling Unit, Department of Biochemistry, University College London, UK
    Curr Opin Struct Biol 9:374-82. 1999
  10. ncbi request reprint From structure to function: approaches and limitations
    J M Thornton
    Biochemistry and Molecular Biology Dept, University College, London, UK
    Nat Struct Biol 7:991-4. 2000

Collaborators

Detail Information

Publications46

  1. ncbi request reprint Classifying a protein in the CATH database of domain structures
    C A Orengo
    Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, Gower St, London WC1E 6BT, England
    Acta Crystallogr D Biol Crystallogr 54:1155-67. 1998
    ..Diagnostic reports are generated, together with multiple structural alignments for close relatives. The Server can be accessed over the World Wide Web (WWW) and mirror sites are planned to improve access...
  2. ncbi request reprint Protein families and their evolution-a structural perspective
    Christine A Orengo
    Department of Biochemistry and Molecular Biology, University College, London WC1E 6BT, United Kingdom
    Annu Rev Biochem 74:867-900. 2005
    ....
  3. pmc The CATH Database provides insights into protein structure/function relationships
    C A Orengo
    Department of Biochemistry and Molecular Biology, Darwin Building, Univeristy College London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 27:275-9. 1999
    ..Our analysis supports the view that determining structures, for example as part of a 'structural genomics' initiative, will make a major contribution to interpreting genome data...
  4. ncbi request reprint The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues
    J E Bray
    Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
    Protein Eng 13:153-65. 2000
    ..The DHS also provides a tool for examining sequence-structure relationships for proteins within each fold group...
  5. pmc A rapid classification protocol for the CATH Domain Database to support structural genomics
    F M Pearl
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 29:223-7. 2001
    ..1997) Nucleic Acids Res., 25, 3389-3402], this provides preliminary classification for easily recognisable homologues, which in the latest release of CATH (version 1.7) represented nearly three-quarters of the non-identical structures...
  6. ncbi request reprint Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction
    C A Orengo
    Department of Biochemistry and Molecular Biology, University College, London, United Kingdom
    Proteins . 1999
    ..However, in combination with other types of prediction data it can sometimes be a useful constraint for identifying the correct structure...
  7. pmc CORA--topological fingerprints for protein structural families
    C A Orengo
    Department of Biochemistry and Molecular Biology, University College, London, United Kingdom
    Protein Sci 8:699-715. 1999
    ..CORA templates for both homologous superfamilies and fold families will be stored in CATH and used to improve the classification and analysis of newly determined structures...
  8. pmc Assigning genomic sequences to CATH
    F M Pearl
    Department of Biochemistry, University College London, University of London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 28:277-82. 2000
    ..The DHS is a powerful tool for considering the variation of functional properties within a given CATH superfamily and in deciding what functional properties may be reliably inherited by a newly identified relative...
  9. ncbi request reprint From protein structure to function
    C A Orengo
    Biomolecular Structure and Modelling Unit, Department of Biochemistry, University College London, UK
    Curr Opin Struct Biol 9:374-82. 1999
    ..g. sequence patterns, common residue clusters and characteristic surface properties)...
  10. ncbi request reprint From structure to function: approaches and limitations
    J M Thornton
    Biochemistry and Molecular Biology Dept, University College, London, UK
    Nat Struct Biol 7:991-4. 2000
    ....
  11. ncbi request reprint Protein folds, functions and evolution
    J M Thornton
    Biochemistry and Molecular Biology Department, University College London, University of London, Gower Street, London, WC1E 6BT, UK
    J Mol Biol 293:333-42. 1999
    ..Such information will provide the foundation to build a better understanding of the molecular basis of biological complexity and hopefully to facilitate rational molecular design...
  12. doi request reprint Systematic computational prediction of protein interaction networks
    J G Lees
    Research Department of Structural and Molecular Biology, University College London, London, UK
    Phys Biol 8:035008. 2011
    ..We describe methods for integrating multiple independent sources of evidence to obtain higher quality predictions and we compare the major publicly available resources available for experimentalists to use...
  13. ncbi request reprint Review: what can structural classifications reveal about protein evolution?
    C A Orengo
    Department of Biochemistry and Molecular Biology, University College, Gower Street, London, WC1E 6BT, United Kingdom
    J Struct Biol 134:145-65. 2001
    ..We also review some more recent analyses that have expanded these classifications by identifying sequence relatives in the genomes and thereby reveal interesting trends in fold usage and recurrence...
  14. pmc FFPred: an integrated feature-based function prediction server for vertebrate proteomes
    A E Lobley
    Department of Computer Science, University College London, London WC1E 6BT, United Kingdom
    Nucleic Acids Res 36:W297-302. 2008
    ..Feature information is provided as easy to interpret graphics displayed on the sequence of interest, allowing for back-interpretation of the associations between features and function classes...
  15. doi request reprint Target selection for structural genomics: an overview
    Russell L Marsden
    Biochemistry and Molecular Biology Department, University College London, London, UK
    Methods Mol Biol 426:3-25. 2008
    ....
  16. doi request reprint The classification of protein domains
    Russell L Marsden
    Biochemistry and Molecular Biology Department, University College London, London, United Kingdom
    Methods Mol Biol 453:123-46. 2008
    ....
  17. ncbi request reprint Structural diversity of domain superfamilies in the CATH database
    Gabrielle A Reeves
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 360:725-41. 2006
    ..Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS)...
  18. ncbi request reprint Protein superfamily evolution and the last universal common ancestor (LUCA)
    Juan A G Ranea
    Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, London, WC1E 6BT, UK
    J Mol Evol 63:513-25. 2006
    ....
  19. pmc The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
    Lesley H Greene
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 35:D291-7. 2007
    ..CATH is directly linked to the Gene3D database which is a projection of CATH structural data onto approximately 2 million sequences in completed genomes and UniProt...
  20. pmc Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
    Russell L Marsden
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
    BMC Bioinformatics 8:86. 2007
    ..It is therefore of considerable interest to gain insights into the number and distribution of these families, and what efforts may be required to achieve a comprehensive structural coverage across all protein families...
  21. pmc The implications of alternative splicing in the ENCODE protein complement
    Michael L Tress
    Structural Computational Biology Programme, Spanish National Cancer Research Centre, E 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 104:5495-500. 2007
    ....
  22. pmc Exploring the structure and function paradigm
    Oliver C Redfern
    Department of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
    Curr Opin Struct Biol 18:394-402. 2008
    ..Obtaining structural data for these functionally coherent groups of proteins will allow us to better understand the relationship between structure and function...
  23. pmc Inferring function using patterns of native disorder in proteins
    Anna Lobley
    Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom
    PLoS Comput Biol 3:e162. 2007
    ..The GO category classifiers generated can be used to provide more reliable predictions and further insights into the behaviour of orphan and unannotated proteins...
  24. pmc LigASite--a database of biologically relevant binding sites in proteins with known apo-structures
    Benoit H Dessailly
    Center for Structural Biology and Bioinformatics, Universite Libre De Bruxelles U L B, Bld du Triomphe CP 263, 1050 Bruxelles, Belgium
    Nucleic Acids Res 36:D667-73. 2008
    ..The datasets can be downloaded from the website as Schema-validated XML files or comma-separated flat files...
  25. pmc CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures
    Oliver C Redfern
    Department of Biochemistry and Molecular Biology, University College London, London, United Kingdom
    PLoS Comput Biol 3:e232. 2007
    ....
  26. pmc Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes
    Juan A G Ranea
    Department of Biochemistry and Molecular Biology, University College London, London, United Kingdom
    PLoS Comput Biol 3:e237. 2007
    ..Our method finds functional relationships that are not detectable by the conventional presence-absence profile comparisons, and it does not require a priori any fixed criteria to define orthologous genes...
  27. pmc ISPIDER Central: an integrated database web-server for proteomics
    Jennifer A Siepen
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Nucleic Acids Res 36:W485-90. 2008
    ..This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics...
  28. pmc Exploiting protein structure data to explore the evolution of protein function and biological complexity
    Russell L Marsden
    Department of Biochemistry, University College London Gower Street, London WC1E 6BT, UK
    Philos Trans R Soc Lond B Biol Sci 361:425-40. 2006
    ....
  29. pmc Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space
    Russell L Marsden
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 34:1066-80. 2006
    ..However, in large families, additional structures should be determined as these would reveal more about the evolution of the family and enable a greater understanding of how function evolves...
  30. pmc Gene3D: modelling protein structure, function and evolution
    Corin Yeats
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
    Nucleic Acids Res 34:D281-4. 2006
    ..Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers...
  31. ncbi request reprint The CATH protein family database: a resource for structural and functional annotation of genomes
    Christine A Orengo
    Department of Biochemistry and Molecular Biology, University College, London, UK
    Proteomics 2:11-21. 2002
    ....
  32. pmc The CATH extended protein-family database: providing structural annotations for genome sequences
    Frances M G Pearl
    Department of Biochemistry and Molecular Biology, University College London, University of London, London WC1E 6BT, UK
    Protein Sci 11:233-44. 2002
    ....
  33. pmc Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database
    Daniel W A Buchan
    Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom
    Genome Res 12:503-14. 2002
    ..Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies...
  34. ncbi request reprint Plasticity of enzyme active sites
    Annabel E Todd
    Biochemistry and Molecular Biology Department, University College London, Gower Street, London, UK WC1E 6BT
    Trends Biochem Sci 27:419-26. 2002
    ....
  35. ncbi request reprint One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions
    Nozomi Nagano
    Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, Gower Street, UK
    J Mol Biol 321:741-65. 2002
    ..This extreme example of the "one fold-many functions" paradigm illustrates the difficulty of assigning function through a structural genomics approach for some folds...
  36. ncbi request reprint PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources
    Adrian J Shepherd
    Department of Biochemistry and Molecular Biology, University College, London, Gower Street, London WC1E 6BT
    Bioinformatics 18:1666-72. 2002
    ....
  37. pmc Gene3D: structural assignments for the biologist and bioinformaticist alike
    Daniel W A Buchan
    Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 31:469-73. 2003
    ..Gene3D is linked to the CATH database and is updated with each new update of CATH...
  38. pmc Target selection and determination of function in structural genomics
    James D Watson
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    IUBMB Life 55:249-55. 2003
    ....
  39. pmc EyeSite: a semi-automated database of protein families in the eye
    David A Lee
    Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
    Nucleic Acids Res 32:D148-52. 2004
    ..The EyeSite is available for online search, sequence information and model retrieval at http://eyesite.cryst.bbk.ac.uk/...
  40. ncbi request reprint Evolution of protein superfamilies and bacterial genome size
    Juan A G Ranea
    Biomlolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, London WC1E 6BT, UK
    J Mol Biol 336:871-87. 2004
    ..For the size-dependent superfamilies, linearly distributed superfamilies are involved mainly in metabolism, and non-linearly distributed superfamily domains are involved principally in gene regulation...
  41. ncbi request reprint A practical and robust sequence search strategy for structural genomics target selection
    James E Bray
    Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
    Bioinformatics 20:2288-95. 2004
    ..With the rapid development of protein comparison software a robust prioritization scheme should be independent of the choice of algorithm and be able to incorporate different sequence similarity thresholds...
  42. ncbi request reprint Microeconomic principles explain an optimal genome size in bacteria
    Juan A G Ranea
    Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, London, UK
    Trends Genet 21:21-5. 2005
    ..This optimum is reached when the bacterial genome obtains the maximum metabolic complexity (revenue) for minimal regulatory genes (logistic cost)...
  43. ncbi request reprint Progress of structural genomics initiatives: an analysis of solved target structures
    Annabel E Todd
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
    J Mol Biol 348:1235-60. 2005
    ..From the perspective of this analysis, it appears that structural genomics is on track to be a success, and it is hoped that this work will inform future directions of the field...
  44. ncbi request reprint Sequence and structural differences between enzyme and nonenzyme homologs
    Annabel E Todd
    Biochemistry and Molecular Biology Department, University College London, United Kingdom
    Structure 10:1435-51. 2002
    ..Heterooligomeric enzymes comprising homologous subunits in which one chain is catalytically inactive and enzyme polypeptides that contain internal catalytic and noncatalytic duplications of an ancient enzyme domain are also discussed...
  45. ncbi request reprint Genomic insights into evolution
    Terry Gaasterland
    Curr Opin Struct Biol 12:345-7. 2002
  46. pmc Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips
    Andrew P Harrison
    Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, UK
    BMC Bioinformatics 8:195. 2007
    ..We wished to establish which of the calibration steps resulted in the biggest uncertainty in the sets of genes reported to be differentially expressed...