Robert D Finn

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes
    Changsoo Chang
    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
    BMC Struct Biol 9:75. 2009
  2. ncbi iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    Robert D Finn
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Bioinformatics 21:410-2. 2005
  3. ncbi The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D211-22. 2010
  4. ncbi Pfam: clans, web tools and services
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nucleic Acids Res 34:D247-51. 2006
  5. ncbi Identifying protein domains with the Pfam database
    Penny Coggill
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Curr Protoc Bioinformatics . 2008
  6. ncbi The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 32:D138-41. 2004
  7. ncbi The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nucleic Acids Res 36:D281-8. 2008
  8. ncbi SCOOP: a simple method for identification of novel protein superfamily relationships
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Bioinformatics 23:809-14. 2007
  9. ncbi InterPro in 2011: new developments in the family and domain prediction database
    Sarah Hunter
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, UK
    Nucleic Acids Res 40:D306-12. 2012
  10. ncbi Pfam 10 years on: 10,000 families and still growing
    Stephen John Sammut
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
    Brief Bioinform 9:210-9. 2008

Detail Information

Publications27

  1. ncbi The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes
    Changsoo Chang
    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
    BMC Struct Biol 9:75. 2009
    ..Streptococcus pyogenes, closely related to LAB, is one of the most common human pathogens, so knowledge of how it competes against other LAB species is likely to prove invaluable...
  2. ncbi iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    Robert D Finn
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Bioinformatics 21:410-2. 2005
    ..sanger.ac.uk/Software/Pfam/iPfam/; the source-data for iPfam is freely available in relational tables via the ftp site ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/...
  3. ncbi The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D211-22. 2010
    ..Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/)...
  4. ncbi Pfam: clans, web tools and services
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nucleic Acids Res 34:D247-51. 2006
    ..Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://pfam.cgb.ki.se/)...
  5. ncbi Identifying protein domains with the Pfam database
    Penny Coggill
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Curr Protoc Bioinformatics . 2008
    ..Details on running Pfam, both remotely and locally are presented...
  6. ncbi The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 32:D138-41. 2004
    ..Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/)...
  7. ncbi The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nucleic Acids Res 36:D281-8. 2008
    ..sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/)...
  8. ncbi SCOOP: a simple method for identification of novel protein superfamily relationships
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Bioinformatics 23:809-14. 2007
    ..Profile searches of sequence databases are a sensitive way to detect sequence relationships. Sophisticated profile-profile comparison algorithms that have been recently introduced increase search sensitivity even further...
  9. ncbi InterPro in 2011: new developments in the family and domain prediction database
    Sarah Hunter
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, UK
    Nucleic Acids Res 40:D306-12. 2012
    ..Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces...
  10. ncbi Pfam 10 years on: 10,000 families and still growing
    Stephen John Sammut
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
    Brief Bioinform 9:210-9. 2008
    ..We also show that as more sequences are added to the sequence databases the fraction of sequences that Pfam matches is reduced, suggesting that continued addition of new families is essential to maintain its relevance...
  11. ncbi Rfam: Wikipedia, clans and the "decimal" release
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA
    Nucleic Acids Res 39:D141-5. 2011
    ..We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk...
  12. ncbi The Pfam protein families database
    Marco Punta
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nucleic Acids Res 40:D290-301. 2012
    ..Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam...
  13. ncbi Integrating sequence and structural biology with DAS
    Andreas Prlic
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    BMC Bioinformatics 8:333. 2007
    ..The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence...
  14. ncbi Predicting active site residue annotations in the Pfam database
    Jaina Mistry
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    BMC Bioinformatics 8:298. 2007
    ....
  15. ncbi Integrating biological data--the Distributed Annotation System
    Andrew M Jenkinson
    European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 9:S3. 2008
    ..DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics...
  16. ncbi Rfam: updates to the RNA families database
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Nucleic Acids Res 37:D136-40. 2009
    ..Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/...
  17. ncbi DUFs: families in search of function
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, England
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1148-52. 2010
    ..In particular, the important role that structural genomics can play in identifying potential function is evaluated...
  18. ncbi 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/)...
  19. ncbi The PASTA domain: a beta-lactam-binding domain
    Corin Yeats
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK CB10 1SA
    Trends Biochem Sci 27:438. 2002
    ..We postulate that PknB-like kinases are key regulators of cell-wall biosynthesis. The essential function of these enzymes suggests an additional pathway for the action of beta-lactam antibiotics...
  20. ncbi Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Bioinformatics 25:159-62. 2009
    ..Common functional features also suggest that tubby and PLSCR share a functional origin as membrane tethered transcription factors with capacity to modulate phosphoinositide-based signaling...
  21. ncbi ProServer: a simple, extensible Perl DAS server
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Geome Campus, Hinxton, Cambridge, UK
    Bioinformatics 23:1568-70. 2007
    ..sanger.ac.uk/proserver/ or CPAN http://search.cpan.org/~rpettett/. Details on the system requirements and installation of ProServer can be found at http://www.sanger.ac.uk/proserver/...
  22. ncbi Making your database available through Wikipedia: the pros and cons
    Robert D Finn
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA, USA
    Nucleic Acids Res 40:D9-12. 2012
    ..Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis...
  23. ncbi Modifier effects between regulatory and protein-coding variation
    Antigone S Dimas
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
    PLoS Genet 4:e1000244. 2008
    ....
  24. ncbi Identification of a functionally impaired allele of human novel oxidoreductase 1 (NDOR1), NDOR1*1
    Robert D Finn
    Cancer Research UK Molecular Pharmacology Unit, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
    Pharmacogenet Genomics 15:381-6. 2005
    ..A variant cDNA sequence of NDOR1, NDOR1 p.518-519ins9 or NDOR1_v1, has been deposited in GenBank (accession no. AK026089 and AY077845) that encodes an additional nine amino acids, which led us to investigate NDOR1 polymorphism...
  25. ncbi Determination of Escherichia coli RNA polymerase structure by single particle cryoelectron microscopy
    Pampa Ray
    Department of Biological Sciences, Wolfson Laboratories, Imperial College of London, Rm. 313, London SW7 2AY, United Kingdom
    Methods Enzymol 370:24-42. 2003
  26. ncbi Determination of the redox potentials and electron transfer properties of the FAD- and FMN-binding domains of the human oxidoreductase NR1
    Robert D Finn
    Biomedical Research Centre, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
    Eur J Biochem 270:1164-75. 2003
    ..Despite overall structural resemblance of NR1 and CPR, our studies reveal thermodynamic similarities but major kinetic differences in the electron transfer reactions catalysed by the flavin-binding domains...
  27. ncbi Conformational changes of Escherichia coli sigma54-RNA-polymerase upon closed-promoter complex formation
    Pampa Ray
    Department of Biological Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
    J Mol Biol 354:201-5. 2005
    ..The binding of DNA leads to significant conformational changes in the enzyme's catalytic subunits, apparently a necessity for the initiation of enhancer-dependent promoter-specific transcription...