Archive Page: Bateman Group | Classification of proteins and RNAs

Archive Page: Bateman Group | Classification of proteins and RNAs

Archive Page: Bateman Group

The Classification of proteins and RNAs group moved to EMBL-EBI (European Molecular Biology Institute-European Bioinformatics Institute) in November 2012. The team continues to work under Alex Bateman, who now leads the EBI's Protein Services. We are maintaining this page as a historical record of the group's activities at the Sanger Institute. For latest information about the group's research, please visit the EMBL-EBI website: http://www.ebi.ac.uk/.

Our Research and Approach

Please note: This page has not been updated since November 2012. Please visit the EMBL-EBI website for the latest information about the group.

The Bateman group sets out to classify proteins and certain RNAs into functional families with a view to producing a 'periodic table' of these molecules.

These classifications allow researchers to rapidly understand the properties and functions of these molecules and thus better interpret their experimental results. The molecules are grouped based on their sequence, structure and function. This group, under the direction of Alex Bateman, has set up a range of different databases that collect and interpret information from researchers around the world. Sophisticated computer programs are applied to sequence information to assist in the classifications. The Pfam and Rfam databases are the most important collections of information for classifying proteins and RNAs, and the MEROPS database provides the worldwide standard nomenclature for peptidase proteins. Alex Bateman also helped initiate the Wikipedia WikiRNA Project. The information acquired is used with the overall view of contributing to the growing understanding of the functions encoded by proteins and RNAs.

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Publications

  • Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors.

    Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A and Söding J

    Bioinformatics (Oxford, England) 2009;25;2;159-62

  • Rfam: updates to the RNA families database.

    Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL et al.

    Nucleic acids research 2009;37;Database issue;D136-40

  • The RNA WikiProject: community annotation of RNA families.

    Daub J, Gardner PP, Tate J, Ramsköld D, Manske M et al.

    RNA (New York, N.Y.) 2008;14;12;2462-4

  • A non-fatal case report of acute fatty liver of pregnancy.

    Kueh YK, Wang TL, Yeo TC and Guan R

    Annals of the Academy of Medicine, Singapore 1991;20;6;789-91

  • MEROPS: the peptidase database.

    Rawlings ND, Morton FR, Kok CY, Kong J and Barrett AJ

    Nucleic acids research 2008;36;Database issue;D320-5

  • Protein interactions in human genetic diseases.

    Schuster-Böckler B and Bateman A

    Genome biology 2008;9;1;R9

  • The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation.

    Bateman A, Holden MT and Yeats C

    Bioinformatics (Oxford, England) 2005;21;8;1301-3

  • The PASTA domain: a beta-lactam-binding domain.

    Yeats C, Finn RD and Bateman A

    Trends in biochemical sciences 2002;27;9;438

  • Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain.

    Cerutti L, Mian N and Bateman A

    Trends in biochemical sciences 2000;25;10;481-2

  • MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.

    Rawlings ND, Waller M, Barrett AJ and Bateman A

    Nucleic acids research 2014;42;Database issue;D503-9

  • Pfam: the protein families database.

    Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY et al.

    Nucleic acids research 2014;42;Database issue;D222-30

  • Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.

    Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P et al.

    BMC bioinformatics 2014;15;75

  • TreeFam v9: a new website, more species and orthology-on-the-fly.

    Schreiber F, Patricio M, Muffato M, Pignatelli M and Bateman A

    Nucleic acids research 2014;42;Database issue;D922-5

  • The COMBREX Project: Design, Methodology, and Initial Results.

    Anton BP, Chang YC, Brown P, Choi HP, Faller LL et al.

    PLoS biology 2013;11;8;e1001638

  • A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.

    Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK et al.

    Nucleic acids research 2013;41;8;4549-64

  • Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.

    Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S et al.

    Genome biology 2013;14;2;R11

  • The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission.

    Tewari R, Straschil U, Bateman A, Böhme U, Cherevach I et al.

    Cell host & microbe 2010;8;4;377-87

  • DUFs: families in search of function.

    Bateman A, Coggill P and Finn RD

    Acta crystallographica. Section F, Structural biology and crystallization communications 2010;66;Pt 10;1148-52

  • Curators of the world unite: the International Society of Biocuration.

    Bateman A

    Bioinformatics (Oxford, England) 2010;26;8;991

  • MEROPS: the peptidase database.

    Rawlings ND, Barrett AJ and Bateman A

    Nucleic acids research 2010;38;Database issue;D227-33

  • Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors.

    Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A and Söding J

    Bioinformatics (Oxford, England) 2009;25;2;159-62

  • Rfam: updates to the RNA families database.

    Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL et al.

    Nucleic acids research 2009;37;Database issue;D136-40

  • The RNA WikiProject: community annotation of RNA families.

    Daub J, Gardner PP, Tate J, Ramsköld D, Manske M et al.

    RNA (New York, N.Y.) 2008;14;12;2462-4

  • Identifying protein domains with the Pfam database.

    Coggill P, Finn RD and Bateman A

    Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2008;Chapter 2;Unit 2.5

  • Pfam 10 years on: 10,000 families and still growing.

    Sammut SJ, Finn RD and Bateman A

    Briefings in bioinformatics 2008;9;3;210-9

  • Large-scale screening for novel low-affinity extracellular protein interactions.

    Bushell KM, Söllner C, Schuster-Boeckler B, Bateman A and Wright GJ

    Genome research 2008;18;4;622-30

  • Protein interactions in human genetic diseases.

    Schuster-Böckler B and Bateman A

    Genome biology 2008;9;1;R9

  • MEROPS: the peptidase database.

    Rawlings ND, Morton FR, Kok CY, Kong J and Barrett AJ

    Nucleic acids research 2008;36;Database issue;D320-5

  • SCOOP: a simple method for identification of novel protein superfamily relationships.

    Bateman A and Finn RD

    Bioinformatics (Oxford, England) 2007;23;7;809-14

  • Visualizing profile-profile alignment: pairwise HMM logos.

    Schuster-Böckler B and Bateman A

    Bioinformatics (Oxford, England) 2005;21;12;2912-3

  • The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation.

    Bateman A, Holden MT and Yeats C

    Bioinformatics (Oxford, England) 2005;21;8;1301-3

  • Rfam: annotating non-coding RNAs in complete genomes.

    Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR and Bateman A

    Nucleic acids research 2005;33;Database issue;D121-4

  • The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases.

    Dillon SC and Bateman A

    BMC bioinformatics 2004;5;109

  • Rfam: an RNA family database.

    Griffiths-Jones S, Bateman A, Marshall M, Khanna A and Eddy SR

    Nucleic acids research 2003;31;1;439-41

  • QuickTree: building huge Neighbour-Joining trees of protein sequences.

    Howe K, Bateman A and Durbin R

    Bioinformatics (Oxford, England) 2002;18;11;1546-7

  • The PASTA domain: a beta-lactam-binding domain.

    Yeats C, Finn RD and Bateman A

    Trends in biochemical sciences 2002;27;9;438

  • Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).

    Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR et al.

    Nature 2002;417;6885;141-7

  • Initial sequencing and analysis of the human genome.

    Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC et al.

    Nature 2001;409;6822;860-921

  • Mining the draft human genome.

    Birney E, Bateman A, Clamp ME and Hubbard TJ

    Nature 2001;409;6822;827-8

  • Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain.

    Cerutti L, Mian N and Bateman A

    Trends in biochemical sciences 2000;25;10;481-2

  • Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.

    Bateman A, Birney E, Durbin R, Eddy SR, Finn RD and Sonnhammer EL

    Nucleic acids research 1999;27;1;260-2