Robert D Finn

Summary

Affiliation: Howard Hughes Medical Institute
Country: USA

Publications

  1. pmc 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
  2. pmc HMMER web server: interactive sequence similarity searching
    Robert D Finn
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
    Nucleic Acids Res 39:W29-37. 2011
  3. pmc 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. pmc 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. pmc 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
  6. doi request reprint 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
  7. pmc 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
  8. pmc 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
  9. pmc Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
    Jaina Mistry
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 41:e121. 2013
  10. pmc 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

Detail Information

Publications29

  1. pmc 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...
  2. pmc HMMER web server: interactive sequence similarity searching
    Robert D Finn
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
    Nucleic Acids Res 39:W29-37. 2011
    ....
  3. pmc 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. pmc 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. pmc 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/)...
  6. doi request reprint 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...
  7. pmc 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...
  8. pmc 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...
  9. pmc Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
    Jaina Mistry
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 41:e121. 2013
    ..They also highlight the need for developing new methods that can correct for this particular type of compositional bias...
  10. pmc 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...
  11. pmc 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...
  12. doi request reprint 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...
  13. pmc 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...
  14. pmc 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/...
  15. pmc 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. pmc Pfam: the protein families database
    Robert D Finn
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147 USA, European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK, Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 Viikinkaari 5, 00014 Helsinki, Finland and Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE 17121 Solna, Sweden
    Nucleic Acids Res 42:D222-30. 2014
    ..Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures. ..
  17. pmc iPfam: a database of protein family and domain interactions found in the Protein Data Bank
    Robert D Finn
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn VA 20147 USA and European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 42:D364-73. 2014
    ..iPfam (version 1.0) contains >9500 domain-domain and 15 500 domain-ligand interactions. The new website provides access to this data in a variety of ways, including interactive visualizations of the interaction data. ..
  18. pmc Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models
    Travis J Wheeler
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    BMC Bioinformatics 15:7. 2014
    ....
  19. pmc The challenge of increasing Pfam coverage of the human proteome
    Jaina Mistry
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Database (Oxford) 2013:bat023. 2013
    ..New families will also be built, prioritizing those that have been experimentally functionally characterized. Database URL: http://pfam.sanger.ac.uk/..
  20. pmc 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
    ....
  21. pmc 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/)...
  22. pmc 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...
  23. pmc 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
    ....
  24. 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/)...
  25. pmc 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/...
  26. pmc Dfam: a database of repetitive DNA based on profile hidden Markov models
    Travis J Wheeler
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Nucleic Acids Res 41:D70-82. 2013
    ..5%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps...
  27. pmc 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
    ....
  28. pmc Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila
    Penelope Coggill
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    BMC Bioinformatics 14:265. 2013
    ..Many of these uncharacterized proteins fall into related sequence families. By applying sequence and structural analysis we hope to provide insight into novel biology...
  29. ncbi request reprint 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...