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Pfam: clans, web tools and services
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SA, UK 1Center for Genomics and Bioinformatics, Karolinska Institutet S-171 77 Stockholm, Sweden 2Department of Genetics, Howard Hughes Medical Institute, Washington University School of Medicine St Louis, MO 63110, USA
*To whom correspondence should be addressed. Tel: +44 1223 495330; Fax: +44 1223 494919; Email: rdf{at}sanger.ac.uk
Received September 15, 2005. Revised October 19, 2005. Accepted October 28, 2005.
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. 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/).
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J. E. Mabey Gilsenan, G. Atherton, J. Bartholomew, P. F. Giles, T. K. Attwood, D. W. Denning, and P. Bowyer Aspergillus Genomes and the Aspergillus Cloud Nucleic Acids Res., January 1, 2009; 37(suppl_1): D509 - D514. [Abstract] [Full Text] [PDF]
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A. J. Bordner Predicting small ligand binding sites in proteins using backbone structure Bioinformatics, December 15, 2008; 24(24): 2865 - 2871. [Abstract] [Full Text] [PDF]
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J.-P. Gagne, M. Isabelle, K. S. Lo, S. Bourassa, M. J. Hendzel, V. L. Dawson, T. M. Dawson, and G. G. Poirier Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes Nucleic Acids Res., December 1, 2008; 36(22): 6959 - 6976. [Abstract] [Full Text] [PDF]
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M.-C. Shun, Y. Botbol, X. Li, F. Di Nunzio, J. E. Daigle, N. Yan, J. Lieberman, M. Lavigne, and A. Engelman Identification and Characterization of PWWP Domain Residues Critical for LEDGF/p75 Chromatin Binding and Human Immunodeficiency Virus Type 1 Infectivity J. Virol., December 1, 2008; 82(23): 11555 - 11567. [Abstract] [Full Text] [PDF]
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D. Chalkia, N. Nikolaidis, W. Makalowski, J. Klein, and M. Nei Origins and Evolution of the Formin Multigene Family That Is Involved in the Formation of Actin Filaments Mol. Biol. Evol., December 1, 2008; 25(12): 2717 - 2733. [Abstract] [Full Text] [PDF]
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K. Fukui, N. Nakagawa, Y. Kitamura, Y. Nishida, R. Masui, and S. Kuramitsu Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression J. Biol. Chem., November 28, 2008; 283(48): 33417 - 33427. [Abstract] [Full Text] [PDF]
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A. J. Robinson, C. Overy, and E. R. S. Kunji The mechanism of transport by mitochondrial carriers based on analysis of symmetry PNAS, November 18, 2008; 105(46): 17766 - 17771. [Abstract] [Full Text] [PDF]
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Y. Zhang, J. Ju, H. Peng, F. Gao, C. Zhou, Y. Zeng, Y. Xue, Y. Li, B. Henrissat, G. F. Gao, et al. Biochemical and Structural Characterization of the Intracellular Mannanase AaManA of Alicyclobacillus acidocaldarius Reveals a Novel Glycoside Hydrolase Family Belonging to Clan GH-A J. Biol. Chem., November 14, 2008; 283(46): 31551 - 31558. [Abstract] [Full Text] [PDF]
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E. B. Rosenblum, J. E. Stajich, N. Maddox, and M. B. Eisen Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis PNAS, November 4, 2008; 105(44): 17034 - 17039. [Abstract] [Full Text] [PDF]
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M. F. Del Papa and M. Perego Ethanolamine Activates a Sensor Histidine Kinase Regulating Its Utilization in Enterococcus faecalis J. Bacteriol., November 1, 2008; 190(21): 7147 - 7156. [Abstract] [Full Text] [PDF]
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R. F. de Souza, V. Anantharaman, S. J. de Souza, L. Aravind, and F. J. Gueiros-Filho AMIN domains have a predicted role in localization of diverse periplasmic protein complexes Bioinformatics, November 1, 2008; 24(21): 2423 - 2426. [Abstract] [Full Text] [PDF]
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