The Pfam protein families database
Open accessAbstract
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. 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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Pfam composition, Gene Ontology and KEGG were used to further validate P. bachei orthologues.
“Pfam composition 54 , Gene Ontology 51 and KEGG 52,53 were used to further validate P. bachei orthologues.”
From The ctenophore genome and the evolutionary origins of neural systems (2014) · cites this paper as [54]
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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Kraulis, P. J. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891004399 · Cited by 14,157 · see citing works
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
Boeckmann, B. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg095 · Cited by 3,894 · see citing works
RASMOL: biomolecular graphics for all
Sayle, R. A. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89080-5 · Cited by 2,587 · see citing works
The Pfam Protein Families Database
Bateman, A. G. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.263 · Cited by 1,253 · see citing works
Self-citationPDBsum: summaries and analyses of PDB structures
Laskowski, R. A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.221 · Cited by 855 · see citing works
Recent improvements to the SMART domain-based sequence annotation resource
Letunić, I. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.242 · Cited by 679 · see citing works
ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons
Corpet, F. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.267 · Cited by 366 · see citing works
The CATH database: an extended protein family resource for structural and functional genomics
Pearl, F. M. G. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg062 · Cited by 263 · see citing works
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database
Boutselakis, H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg065 · Cited by 105 · see citing works
Enhanced protein domain discovery by using language modeling techniques from speech recognition
Coin, L., Bateman, A. G., & Durbin, R. M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0737502100 · Cited by 60 · see citing works
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Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G. V., Clark, N. R., & Ma’ayan, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-128 · Cited by 7,814 · see citing works
Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080 · see citing works
Pfam: the protein families database
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148 · see citing works
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International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750 · see citing works
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Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017) · Nature · doi:10.1038/nature22043 · Cited by 1,450 · see citing works
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
MacArthur, D. G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K., Jostins, L., Habegger, L., Pickrell, J. K., Montgomery, S. B., et al. (2012) · Science · doi:10.1126/science.1215040 · Cited by 1,272 · see citing works
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King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139 · see citing works
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Ross, M. T., Grafham, D. V., Coffey, A. J., Scherer, S., McLay, K., Muzny, D., Platzer, M., Howell, G. R., Burrows, C., Bird, C. P., et al. (2005) · Nature · doi:10.1038/nature03440 · Cited by 1,129 · see citing works
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Ohgami, R. S., Campagna, D. R., Greer, E. L., Antiochos, B., McDonald, A., Chen, J., Sharp, J. J., Fujiwara, Y., Barker, J. E., & Fleming, M. D. (2005) · Nature Genetics · doi:10.1038/ng1658 · Cited by 775 · see citing works
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Andreini, C., Banci, L., Bertini, I., & Rosato, A. (2006) · Journal of Proteome Research · doi:10.1021/pr0603699 · Cited by 648 · see citing works
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Minezaki, Y., Homma, K., Kinjo, A. R., & Nishikawa, K. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.04.016 · Cited by 297 · see citing works
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Wall, T., Båth, K., Britton, R. A., Jonsson, H., Versalovic, J., & Roos, S. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01502-06 · Cited by 131 · see citing works
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Hao, P., Zheng, H., Yu, Y., Ding, G., Gu, W., Chen, S., Yu, Z., Ren, S., Oda, M., Konno, T., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0015964 · Cited by 100 · see citing works
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“Sequences were compared to KO pro fi les within the KEGG Automatic AnnotationServer(KAAS,downloadedApril2019)(KAAS;downloaded April 2019) 114 , to COG pro fi les within the NCBI COG database (down-loaded May 2020) 115 – 117 , and to Pfam pro fi les in the Pfam database (Release 34.0) 118 .”
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- Authors
- Bateman, A.
- Affiliations
- Wellcome Sanger Institute (GB)
- Corresponding author
- Bateman, A.
- ORCID
- Bateman, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-01-01
- Volume
- 32
- Issue
- 90001
- Pages
- 138D-141
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC308855
- OpenAlex
- W4210400672
- Cited by
- 3,127
- References
- 10
- Citations by year
- 2026: 50 · 2025: 97 · 2024: 120 · 2023: 94 · 2022: 124 · 2021: 145 · 2020: 102 · 2019: 103 · 2018: 93 · 2017: 89 · 2016: 76 · 2015: 92 · 2014: 81 · 2013: 75 · 2012: 92
- FWCI
- 105.06
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (submittedVersion, cc-by)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Funders
- Wellcome Trust
- Medical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- Pfam, protein families, protein domains, domain modeling, protein sequence databases, web search interfaces, structure database
- MeSH terms
- Animals, Multigene Family, Humans, Models, Molecular, Proteins, Protein Structure, Tertiary, Computational Biology, Internet, Databases, Protein
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