J Gough

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. pmc SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
    Julian Gough
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 30:268-72. 2002
  2. ncbi request reprint Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    J Gough
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 313:903-19. 2001
  3. ncbi request reprint Domain combinations in archaeal, eubacterial and eukaryotic proteomes
    G Apic
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 310:311-25. 2001
  4. ncbi request reprint The SUPERFAMILY database in structural genomics
    Julian Gough
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
    Acta Crystallogr D Biol Crystallogr 58:1897-900. 2002
  5. pmc New developments in the InterPro database
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute Hinxton, Cambridge, UK
    Nucleic Acids Res 35:D224-8. 2007
  6. ncbi request reprint Evolution of the protein repertoire
    Cyrus Chothia
    Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 300:1701-3. 2003
  7. ncbi request reprint The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli
    S A Teichmann
    Department of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
    J Mol Biol 311:693-708. 2001
  8. ncbi request reprint Small-molecule metabolism: an enzyme mosaic
    S A Teichmann
    Dept of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, UK
    Trends Biotechnol 19:482-6. 2001
  9. ncbi request reprint Supra-domains: evolutionary units larger than single protein domains
    Christine Vogel
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 336:809-23. 2004
  10. pmc InterPro, progress and status in 2005
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 33:D201-5. 2005

Detail Information

Publications30

  1. pmc SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
    Julian Gough
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 30:268-72. 2002
    ..The database is currently used by this group and others for genome annotation, structural genomics, gene prediction and domain-based genomic studies...
  2. ncbi request reprint Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    J Gough
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 313:903-19. 2001
    ..The annotations derived from these matches are available from a public web server at: http://stash.mrc-lmb.cam.ac.uk/SUPERFAMILY. This server also enables users to match their own sequences against the SUPERFAMILY model library...
  3. ncbi request reprint Domain combinations in archaeal, eubacterial and eukaryotic proteomes
    G Apic
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 310:311-25. 2001
    ..Finally, we compare the set of the domain combinations in the genomes to those in the RCSB Protein Data Bank, and discuss the implications for structural genomics...
  4. ncbi request reprint The SUPERFAMILY database in structural genomics
    Julian Gough
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
    Acta Crystallogr D Biol Crystallogr 58:1897-900. 2002
    ..The database provides evolutionary relationships between target proteins and other proteins of known structure through the SCOP database, genome assignments and multiple sequence alignments...
  5. pmc New developments in the InterPro database
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute Hinxton, Cambridge, UK
    Nucleic Acids Res 35:D224-8. 2007
    ..ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html...
  6. ncbi request reprint Evolution of the protein repertoire
    Cyrus Chothia
    Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 300:1701-3. 2003
    ..Proteins of known structure can be matched to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins of these processes...
  7. ncbi request reprint The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli
    S A Teichmann
    Department of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
    J Mol Biol 311:693-708. 2001
    ..Most of the domains that form SMM pathways have homologues in non-SMM pathways. Taken together, these results imply a pervasive "mosaic" model for the formation of protein repertoires and pathways...
  8. ncbi request reprint Small-molecule metabolism: an enzyme mosaic
    S A Teichmann
    Dept of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, UK
    Trends Biotechnol 19:482-6. 2001
    ..This is analogous to a mosaic in which a stone of a certain colour is selected to fill a position in the picture...
  9. ncbi request reprint Supra-domains: evolutionary units larger than single protein domains
    Christine Vogel
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 336:809-23. 2004
    ..Since this is the case for only a quarter of the supra-domains, we provide a list of the most important unknown supra-domains as potential targets for structural genomics projects...
  10. pmc InterPro, progress and status in 2005
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 33:D201-5. 2005
    ..The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  11. pmc A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Bacteriol 188:2761-73. 2006
    ..The website, along with additional information on the biosynthetic pathway, statistics on predicted lipoproteins, and related figures, is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop/...
  12. pmc The SUPERFAMILY database in 2007: families and functions
    Derek Wilson
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 35:D308-13. 2007
    ..The SUPERFAMILY database can be used for general protein evolution and superfamily-specific studies, genomic annotation, and structural genomics target suggestion and assessment...
  13. pmc SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
    Derek Wilson
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK
    Nucleic Acids Res 37:D380-6. 2009
    ..The database, models and associated scripts are available for download from the ftp site...
  14. pmc The SUPERFAMILY database in 2004: additions and improvements
    Martin Madera
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 32:D235-9. 2004
    ..In addition, the webserver provides the following standard services: sequence search; keyword search for genomes, superfamilies and sequence identifiers; and multiple alignment of genomic, PDB and custom sequences...
  15. pmc Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor
    Ermanno Gherardi
    Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom
    Proc Natl Acad Sci U S A 100:12039-44. 2003
    ..Our studies provide 3D models and a functional map of the MET ectodomain. They have broad implications for structure-function of the MET receptor and the related semaphorin and plexin proteins...
  16. doi request reprint Genomic and structural aspects of protein evolution
    Cyrus Chothia
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Biochem J 419:15-28. 2009
    ..We conclude with a brief note on other forms of protein evolution and speculations of the origins of the duplication, divergence and combination processes...
  17. pmc A comparison of profile hidden Markov model procedures for remote homology detection
    Martin Madera
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 30:4321-8. 2002
    ..It was found that the SAM T99 iterative database search procedure performs better than the most recent version of PSI-BLAST, but that scoring of PSI-BLAST profiles is more than 30 times faster than scoring of SAM models...
  18. ncbi request reprint An insight into domain combinations
    G Apic
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
    Bioinformatics 17:S83-9. 2001
    ..This type of pattern can be described by a scale-free network. Finally, we study domain repeats and we compare the set of the domain combinations in the genomes to those in PDB, and discuss the implications for structural genomics...
  19. pmc InterPro: the integrative protein signature database
    Sarah Hunter
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 37:D211-5. 2009
    ..InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/)...
  20. ncbi request reprint Proteins with class alpha/beta fold have high-level participation in fusion events
    Sujun Hua
    Institute of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, People s Republic of China
    J Mol Biol 320:713-9. 2002
    ..c) 2002 Elsevier Science Ltd...
  21. pmc Genomic scale sub-family assignment of protein domains
    Julian Gough
    Unite de Bioinformatique Structurale, Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, Paris, France
    Nucleic Acids Res 34:3625-33. 2006
    ..Hence it has already been applied at the SCOP family level to all genomes in the SUPERFAMILY database, providing a wealth of new data to the biological and bioinformatics communities...
  22. ncbi request reprint Convergent evolution of domain architectures (is rare)
    Julian Gough
    RIKEN Genomic Sciences Centre, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Bioinformatics 21:1464-71. 2005
    ..We use a range of methods including phylogenetic grouping, sequence similarity/alignment, mutation rates and comparative genomics to approach this difficult problem from several angles...
  23. pmc A phylogenomic profile of globins
    Serge N Vinogradov
    Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
    BMC Evol Biol 6:31. 2006
    ..The single-domain globins encompass sequences related to chimeric globins and "truncated" hemoglobins with a 2-over-2 instead of the canonical 3-over-3 alpha-helical fold...
  24. ncbi request reprint The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins
    Julian Gough
    RIKEN Genomic Sciences Centre, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Structure 12:917-25. 2004
    ..Residues around the active site are conserved for functional reasons, while those deeper in the structure will be conserved for structural reasons. Together the two sets support each other...
  25. pmc Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life
    Serge N Vinogradov
    Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 102:11385-9. 2005
    ..Furthermore, it appears likely that the predominant functions of globins are enzymatic and that oxygen transport is a specialized development that accompanied the evolution of metazoans...
  26. pmc Mouse proteome analysis
    Alexander Kanapin
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Genome Res 13:1335-44. 2003
    ..The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins..
  27. pmc Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae
    Oliver Jardine
    Department of Crystallography, Birkbeck College, London WC1E 7HX, United Kingdom
    Genome Res 12:916-29. 2002
    ..Only one fifth of the common enzymes have nonhomologous domains between the two organisms. Around the common core very different extensions have been made to small molecule metabolism in the two organisms...
  28. pmc Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs
    Norihiro Maeda
    Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
    PLoS Genet 2:e62. 2006
    ....
  29. pmc Development and evaluation of an automated annotation pipeline and cDNA annotation system
    Takeya Kasukawa
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Res 13:1542-51. 2003
    ....
  30. pmc Distinguishing protein-coding from non-coding RNAs through support vector machines
    Jinfeng Liu
    Columbia University Bioinformatics Center, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
    PLoS Genet 2:e29. 2006
    ..Applied to 102,801 mouse cDNAs from the FANTOM3 dataset, our method reliably identified over 14,000 ncRNAs and estimated the total number of ncRNAs to be about 28,000...