Citing Pfam

Latest publications

The Pfam protein families database: embracing AI/ML T. Paysan-Lafosse, A. Andreeva, M. Blum, S. Chuguransky, T. Grego, B. Lazaro Pinto, G.A. Salazar, M.L. Bileschi, F. Llinares-López, L. Meng-Papaxanthos, L.J. Colwell, NV. Grishin, R.D. Schaeffer, D.Clementel, S.C.E Tosatto, E. Sonnhammer, V. Wood, A. Bateman Nucleic Acids Research (2024) doi: 10.1093/nar/gkae997, PMID: 39540428

Bridging the gap between sequence and structure classifications of proteins with AlphaFold models. J. Pei, A. Andreeva, S. Chuguransky, B. Lázaro Pinto, T. Paysan-Lafosse, D.R. Schaeffer, A. Bateman, Q. Cong, NV. Grishin Journal of Molecular Biology (2024) doi: 10.1016/j.jmb.2024.168764, PMID: 39197652

Previous publications

Pfam: The protein families database in 2021 J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G.A. Salazar, E.L.L. Sonnhammer, S.C.E. Tosatto, L. Paladin, S. Raj, L.J. Richardson, R.D. Finn, A. Bateman Nucleic Acids Research (2020) Database Issue 49:D412–D419, PMID: 33125078

The Pfam protein families database in 2019: S. El-Gebali, J. Mistry, A. Bateman, S.R. Eddy, A. Luciani, S.C. Potter, M. Qureshi, L.J. Richardson, G.A. Salazar, A. Smart, E.L.L. Sonnhammer, L. Hirsh, L. Paladin, D. Piovesan, S.C.E. Tosatto, R.D. Finn Nucleic Acids Research (2019) Database Issue 47:D427–D432, PMID: 30357350

The Pfam protein families database: towards a more sustainable future: R.D. Finn, P. Coggill, R.Y. Eberhardt, S.R. Eddy, J. Mistry, A.L. Mitchell, S.C. Potter, M. Punta, M. Qureshi, A. Sangrador-Vegas, G.A. Salazar, J. Tate, A. Bateman Nucleic Acids Research (2016) Database Issue 44:D279-D285, PMID: 26673716

The Pfam protein families database: R.D. Finn, A. Bateman, J. Clements, P. Coggill, R.Y. Eberhardt, S.R. Eddy, A. Heger, K. Hetherington, L. Holm, J. Mistry, E.L.L. Sonnhammer, J. Tate, M. Punta Nucleic Acids Research (2014) Database Issue 42:D222-D230, PMID: 24288371

The Pfam protein families database: M. Punta, P.C. Coggill, R.Y. Eberhardt, J. Mistry, J. Tate, C. Boursnell, N. Pang, K. Forslund, G. Ceric, J. Clements, A. Heger, L. Holm, E.L.L. Sonnhammer, S.R. Eddy, A. Bateman, R.D. Finn Nucleic Acids Research (2012) Database Issue 40:D290-D301, PMID: 22127870

The Pfam protein families database: R.D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J.E. Pollington, O.L. Gavin, P. Gunesekaran, G. Ceric, K. Forslund, L. Holm, E.L. Sonnhammer, S.R. Eddy, A. Bateman Nucleic Acids Research (2010) Database Issue 38:D211-D222, PMID: 19920124

The Pfam protein families database: R.D. Finn, J. Tate, J. Mistry, P.C. Coggill, J.S. Sammut, H.R. Hotz, G. Ceric, K. Forslund, S.R. Eddy, E.L. Sonnhammer and A. Bateman Nucleic Acids Research (2008) Database Issue 36:D281-D288

Pfam: clans, web tools and services: R.D. Finn, J. Mistry, B. Schuster-Böckler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S.R. Eddy, E.L.L. Sonnhammer and A. Bateman Nucleic Acids Research (2006) Database Issue 34:D247-D51

Enhanced protein domain discovery by using language modeling techniques from speech recognition: L. Coin, A. Bateman and R. Durbin Proc. Natl. Acad. Sci. USA. (2003) 100(8):4516-20

The Pfam Protein Families Database: A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E.L.L. Sonnhammer, D.J. Studholme, C. Yeats and S.R. Eddy Nucleic Acids Research (2004) 32:D138-D141

The Pfam Protein Families Database: A. Bateman, E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S.R. Eddy, S. Griffiths-Jones, K.L. Howe, M. Marshall and E.L. Sonnhammer Nucleic Acids Research (2002) 30(1):276-280

The Pfam Protein Families Database: A. Bateman, E. Birney, R. Durbin, S.R. Eddy, K.L. Howe and E.L. Sonnhammer Nucleic Acids Research (2000) 28:263-266

Pfam 3.1: 1313 multiple alignments match the majority of proteins: A. Bateman, E. Birney, R. Durbin, S.R. Eddy, R.D. Finn and E.L.L. Sonnhammer Nucleic Acids Research (1999) 27:260-262

Pfam: multiple sequence alignments and HMM-profiles of protein domains: E.L.L. Sonnhammer, S.R. Eddy, E. Birney, A. Bateman and R. Durbin Nucleic Acids Research (1998) 26:320-322

Pfam: a comprehensive database of protein families based on seed alignments: E.L.L. Sonnhammer, S.R. Eddy and R. Durbin Proteins (1997) 28:405-420

Book Chapters on Pfam

Homology-Based Annotation of Large Protein Datasets M. Punta, J. Mistry Data Mining Techniques for the Life Sciences. Methods in Molecular Biology vol 1415 (2016) doi: 10.1007/978-1-4939-3572-7_8

Identifying Protein Domains with the Pfam Database P. Coggill, R.D. Finn, A. Bateman Current Protocols in Bioinformatics Chapter 2, Unit 2.5 (2008) doi: 10.1002/0471250953.bi0205s23

Pfam: a domain-centric method for analysing proteins and proteomes J. Mistry and R.D. Finn Comparative Genomics. Methods in Molecular Biology vol 396 (2007) doi: 10.1007/978-1-59745-515-2_4

Pfam: the protein families database R.D. Finn (eds M.J. Dunn, L.B. Jorde, P.F.R. Little, S. Subramaniam) Genetics, Genomics, Proteomics and Bioinformatics, Section 6: Protein Families (2005) doi: 10.1002/047001153X.g306303

Identifying protein domains with the Pfam database R.D. Finn, A. Bateman and S. Griffiths-Jones Current Protocols in Bioinformatics (2003) doi: 10.1002/0471250953.bi0205s01