Alex Bateman

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi The CHAP domain: a large family of amidases including GSP amidase and peptidoglycan hydrolases
    Alex Bateman
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK CB10 1SA
    Trends Biochem Sci 28:234-7. 2003
  2. pmc Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain
    William Mifsud
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Genome Biol 3:RESEARCH0068. 2002
  3. pmc 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
  4. pmc Structure and distribution of pentapeptide repeats in bacteria
    A Bateman
    Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
    Protein Sci 7:1477-80. 1998
  5. 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
  6. pmc The TROVE module: a common element in Telomerase, Ro and Vault ribonucleoproteins
    Alex Bateman
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    BMC Bioinformatics 4:49. 2003
  7. 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
  8. 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
  9. ncbi The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation
    Alex Bateman
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 21:1301-3. 2005
  10. pmc Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
    A Bateman
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 27:260-2. 1999

Detail Information

Publications76

  1. ncbi The CHAP domain: a large family of amidases including GSP amidase and peptidoglycan hydrolases
    Alex Bateman
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK CB10 1SA
    Trends Biochem Sci 28:234-7. 2003
    ..The large number of multifunctional hydrolases suggests that they might act in a cooperative manner to cleave specialized substrates...
  2. pmc Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain
    William Mifsud
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Genome Biol 3:RESEARCH0068. 2002
    ..They do not show sequence similarity to any of the classical steroid receptors. We were interested in identifying distant homologs of MAPR better to understand their biological roles...
  3. pmc 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...
  4. pmc Structure and distribution of pentapeptide repeats in bacteria
    A Bateman
    Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
    Protein Sci 7:1477-80. 1998
    ..A structural model of the pentapeptide repeats is presented...
  5. 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...
  6. pmc The TROVE module: a common element in Telomerase, Ro and Vault ribonucleoproteins
    Alex Bateman
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    BMC Bioinformatics 4:49. 2003
    ..Ribonucleoproteins carry out a variety of important tasks in the cell. In this study we show that a number of these contain a novel module, that we speculate mediates RNA-binding...
  7. 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/)...
  8. 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
    ....
  9. ncbi The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation
    Alex Bateman
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 21:1301-3. 2005
    ..A common feature of the proteins containing G5 domains is N-acetylglucosamine binding, and we attribute this function to the G5 domain...
  10. pmc Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
    A Bateman
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 27:260-2. 1999
    ..1 are that we now use the more advanced version 2 of the HMMER software, which is more sensitive and provides expectation values for matches, and that it now includes proteins from both SP-TrEMBL and SWISS-PROT...
  11. pmc The Pfam protein families database
    A Bateman
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 28:263-6. 2000
    ..These Pfam families match 63% of proteins in SWISS-PROT 37 and TrEMBL 9. For complete genomes Pfam currently matches up to half of the proteins. Genomic DNA can be directly searched against the Pfam library using the Wise2 package...
  12. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 30:276-80. 2002
    ..New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource...
  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 The SGS3 protein involved in PTGS finds a family
    Alex Bateman
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    BMC Bioinformatics 3:21. 2002
    ..Components of the PTGS machinery are being discovered by genetic and bioinformatics approaches, but the picture is not yet complete...
  15. 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/)...
  16. 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...
  17. 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/)...
  18. 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)...
  19. pmc MEROPS: the peptidase database
    Neil D Rawlings
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D227-33. 2010
    ..This has allowed us to add an analysis tool to the relevant species pages to show significant gains and losses of peptidase genes relative to related species...
  20. doi 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...
  21. 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/)...
  22. pmc The InterPro Database, 2003 brings increased coverage and new features
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 31:315-8. 2003
    ..The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  23. pmc Rfam 11.0: 10 years of RNA families
    Sarah W Burge
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 41:D226-32. 2013
    ..0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license...
  24. ncbi Visualizing profile-profile alignment: pairwise HMM logos
    Benjamin Schuster-Böckler
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 21:2912-3. 2005
    ..The method illustrates the similarities of pairs of protein family profiles in an intuitive way. Two HMM logos, one for each profile, are drawn one upon the other. The aligned states are then highlighted and connected...
  25. 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
    ..The resource called iPfam is hosted within the Pfam UK website. Most resources focus on the interactions between proteins; iPfam includes these as well as interactions between domains in a single protein...
  26. doi Identifying protein domains with the Pfam database
    Robert Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, United Kingdom
    Curr Protoc Bioinformatics . 2003
    ..This unit contains detailed information on how to access and utilise the information present in the Pfam database, namely the families, multiple alignments and annotation. Details on running Pfam, both remotely and locally are presented...
  27. ncbi QuickTree: building huge Neighbour-Joining trees of protein sequences
    Kevin Howe
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Bioinformatics 18:1546-7. 2002
    ..QuickTree allows the reconstruction of phylogenies for very large protein families (including the largest Pfam alignment containing 27000 HIV GP120 glycoprotein sequences) that would be infeasible using other popular methods...
  28. 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/)...
  29. pmc Rfam: annotating non-coding RNAs in complete genomes
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 33:D121-4. 2005
    ..Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/...
  30. doi Filling out the structural map of the NTF2-like superfamily
    Ruth Y Eberhardt
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    BMC Bioinformatics 14:327. 2013
    ..Clues to the function of protein domains belonging to such a diverse superfamily can be gleaned from analysis of the proteins and organisms in which they are found...
  31. pmc Reuse of structural domain-domain interactions in protein networks
    Benjamin Schuster-Böckler
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
    BMC Bioinformatics 8:259. 2007
    ..Here, we investigate how the domain interactions from the iPfam database are distributed in protein interactions taken from the HPRD, MPact, BioGRID, DIP and IntAct databases...
  32. 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...
  33. pmc AntiFam: a tool to help identify spurious ORFs in protein annotation
    Ruth Y Eberhardt
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
    Database (Oxford) 2012:bas003. 2012
    ..UniProt has adopted AntiFam as a part of the UniProtKB quality control process and will investigate these spurious proteins for exclusion...
  34. pmc Enhanced protein domain discovery using taxonomy
    Lachlan Coin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    BMC Bioinformatics 5:56. 2004
    ..This information has not yet been incorporated into statistical methods for finding domains in sequences of amino acids...
  35. doi 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...
  36. ncbi The BON domain: a putative membrane-binding domain
    Corin Yeats
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK CB10 1SA
    Trends Biochem Sci 28:352-5. 2003
  37. 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...
  38. doi 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. ..
  39. 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...
  40. pmc The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases
    Shane C Dillon
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    BMC Bioinformatics 5:109. 2004
    ..strain CBS. Since that time structural determinations have shown a number of other apparently unrelated proteins also share the Hotdog fold...
  41. pmc Rfam: an RNA family database
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 31:439-41. 2003
    ..wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database...
  42. 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...
  43. pmc SnoPatrol: how many snoRNA genes are there?
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB101SA, UK
    J Biol 9:4. 2010
    ..Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA. Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain to be found...
  44. ncbi Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica
    David J Studholme
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    FEMS Microbiol Lett 236:333-40. 2004
    ....
  45. pmc Enhanced protein domain discovery by using language modeling techniques from speech recognition
    Lachlan Coin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
    Proc Natl Acad Sci U S A 100:4516-20. 2003
    ..As an example, we discover an unannotated Tf_Otx Pfam domain on the cone rod homeobox protein, which suggests a possible mechanism for how the V242M mutation on this protein causes cone-rod dystrophy...
  46. doi An introduction to hidden Markov models
    Benjamin Schuster-Böckler
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    Curr Protoc Bioinformatics . 2007
    ..The unit also presents a brief history of hidden Markov models and an overview of their current applications before concluding with a discussion of their limitations...
  47. 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...
  48. 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
    ....
  49. pmc Quantifying the mechanisms of domain gain in animal proteins
    Marija Buljan
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Biol 11:R74. 2010
    ..By using animal gene phylogenies we were able to identify a set of high confidence domain gain events and by looking at their coding DNA investigate the causative mechanisms...
  50. pmc New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor
    Corin Yeats
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    BMC Microbiol 3:3. 2003
    ..We sought to expand our understanding of this organism at the molecular level through identification and annotation of novel protein domains. Protein domains are the evolutionary conserved units from which proteins are formed...
  51. pmc Pepsin homologues in bacteria
    Neil D Rawlings
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    BMC Genomics 10:437. 2009
    ..The presence of a pepsin homologue in a prokaryote might give insights into the evolution of the pepsin family...
  52. ncbi HMM-based databases in InterPro
    Alex Bateman
    Pfam Group, The Wellcome Trust Sanger Institute, Hinxton, UK
    Brief Bioinform 3:236-45. 2002
    ..This paper reviews the Pfam, TIGRFAMs and SMART databases that use the profile-HMMs provided by the HMMER package...
  53. doi The evolution of protein domain families
    Marija Buljan
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Biochem Soc Trans 37:751-5. 2009
    ..We can trace how the structure and sequence of this family diverged during vertebrate evolution into constant and variable domains that are found in the antibodies of our immune system as well as in neural and muscle proteins...
  54. 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/...
  55. ncbi InterPro: an integrated documentation resource for protein families, domains and functional sites
    Nicola J Mulder
    EMBL Outstation, European Bioinformatics Institute, Hinxton, Cambridge, UK
    Brief Bioinform 3:225-35. 2002
    ..Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (2,141,621 InterPro hits from 586,124 SWISS-PROT and TrEMBL protein sequences). The database is freely accessible for text- and sequence-based searches...
  56. pmc RNIE: genome-wide prediction of bacterial intrinsic terminators
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, UK
    Nucleic Acids Res 39:5845-52. 2011
    ..tuberculosis genic elements. The software, predictions and alignments described below are available from http://github.com/ppgardne/RNIE...
  57. 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/..
  58. pmc Asparagine peptide lyases: a seventh catalytic type of proteolytic enzymes
    Neil David Rawlings
    Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    J Biol Chem 286:38321-8. 2011
    ..We have assembled ten families based on sequence similarity in which cleavage is thought to be catalyzed by an asparagine...
  59. ncbi The PepSY domain: a regulator of peptidase activity in the microbial environment?
    Corin Yeats
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Trends Biochem Sci 29:169-72. 2004
  60. ncbi The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 18:1243-9. 2002
    ..The performance of profile HMMs derived from the structural and sequence-based alignments has been assessed for homologue detection...
  61. ncbi The tify family previously known as ZIM
    Bartel Vanholme
    Faculty of Bioscience Engineering, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B 9000 Ghent, Belgium
    Trends Plant Sci 12:239-44. 2007
    ..Furthermore, because of the confusing ZIM nomenclature being used at present, we propose to rename the domain and family as tify, after the most conserved amino acid motif characterizing the members of this family...
  62. pmc Metazoan Scc4 homologs link sister chromatid cohesion to cell and axon migration guidance
    Vlad C Seitan
    Institute of Human Genetics, University of Newcastle, Newcastle upon Tyne, United Kingdom
    PLoS Biol 4:e242. 2006
    ....
  63. pmc A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium
    Lars Barquist
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 41:4549-64. 2013
    ..We are able to assign probable functions to a number of cis-regulatory ncRNA elements, as well as to infer likely differences in trans-acting ncRNA regulatory networks...
  64. pmc Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks
    Marija Buljan
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Mol Cell 46:871-83. 2012
    ..In this way, tissue-specific splicing may contribute to functional versatility of proteins and increases the diversity of interaction networks across tissues...
  65. pmc The YARHG domain: an extracellular domain in search of a function
    Penny Coggill
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS ONE 7:e35575. 2012
    ..The large number of different domains that are found associated with YARHG suggests that it is a useful functional module that nature has recombined multiple times...
  66. pmc MEROPS: the database of proteolytic enzymes, their substrates and inhibitors
    Neil D Rawlings
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 40:D343-50. 2012
    ....
  67. pmc A comparison of Pfam and MEROPS: two databases, one comprehensive, and one specialised
    David J Studholme
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 4:17. 2003
    ..An additional reason for carrying out this study was to explore the extent of consensus in the definition of a protein family...
  68. pmc The characterisation of three types of genes that overlie copy number variable regions
    Cara Woodwark
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS ONE 6:e14814. 2011
    ..We classify these as type I, II and III CNV genes respectively...
  69. pmc Large-scale screening for novel low-affinity extracellular protein interactions
    K Mark Bushell
    Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, United Kingdom
    Genome Res 18:622-30. 2008
    ..This technique will now allow large-scale extracellular protein interaction mapping in a broad range of experimental contexts...
  70. pmc miRBase: microRNA sequences, targets and gene nomenclature
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 34:D140-4. 2006
    ..miRBase Sequences is the primary online repository for miRNA sequence data and annotation. miRBase Targets is a comprehensive new database of predicted miRNA target genes. miRBase is available at http://microrna.sanger.ac.uk/...
  71. doi Databases, data tombs and dust in the wind
    Jonathan D Wren
    Bioinformatics 24:2127-8. 2008
    ..Thus, for database creators, reviewers and journal editors, there are several additional considerations to judge, prior to publication, how potentially valuable these new databases may be...
  72. pmc Biocurators and biocuration: surveying the 21st century challenges
    Sarah Burge
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Database (Oxford) 2012:bar059. 2012
    ..DATABASE URL: http://biocurator.org...
  73. pmc Protein interactions in human genetic diseases
    Benjamin Schuster-Böckler
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Genome Biol 9:R9. 2008
    ..Combining predicted and hand-curated sets, we discuss how mutations affect protein interactions in general...
  74. ncbi The ENTH domain
    Pietro De Camilli
    Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
    FEBS Lett 513:11-8. 2002
    ..The ENTH domain is structurally similar to the VHS domain. These domains define two families of adaptor proteins which function in membrane traffic and whose interaction with membranes is regulated, in part, by phosphoinositides...
  75. 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...
  76. ncbi Structural genomics meets computational biology
    Alex Bateman
    Bioinformatics 22:2319. 2006