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Items: 1 to 20 of 37


The Pfam protein families database: towards a more sustainable future.

Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A.

Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85. doi: 10.1093/nar/gkv1344.


The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.

Chiang Z, Vastermark A, Punta M, Coggill PC, Mistry J, Finn RD, Saier MH Jr.

Brief Bioinform. 2015 Sep;16(5):865-72. doi: 10.1093/bib/bbu053.


Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.

Kumar A, Punta M, Axelrod HL, Das D, Farr CL, Grant JC, Chiu HJ, Miller MD, Coggill PC, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA.

Protein Sci. 2014 Oct;23(10):1380-91. doi: 10.1002/pro.2522.


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, Bateman A, Godzik A, Aravind L.

BMC Bioinformatics. 2014 Mar 19;15:75. doi: 10.1186/1471-2105-15-75.


New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily.

Trame CB, Chang Y, Axelrod HL, Eberhardt RY, Coggill P, Punta M, Rawlings ND.

BMC Bioinformatics. 2014 Jan 3;15:1. doi: 10.1186/1471-2105-15-1.


Pfam: the protein families database.

Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M.

Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30. doi: 10.1093/nar/gkt1223.


LUD, a new protein domain associated with lactate utilization.

Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A.

BMC Bioinformatics. 2013 Nov 26;14:341. doi: 10.1186/1471-2105-14-341.


Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.

Coggill P, Eberhardt RY, Finn RD, Chang Y, Jaroszewski L, Godzik A, Das D, Xu Q, Axelrod HL, Aravind L, Murzin AG, Bateman A.

BMC Bioinformatics. 2013 Sep 3;14:265. doi: 10.1186/1471-2105-14-265.


The challenge of increasing Pfam coverage of the human proteome.

Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD, Bateman A, Punta M.

Database (Oxford). 2013 Apr 19;2013:bat023. doi: 10.1093/database/bat023.


Sequencing and comparative analysis of the gorilla MHC genomic sequence.

Wilming LG, Hart EA, Coggill PC, Horton R, Gilbert JG, Clee C, Jones M, Lloyd C, Palmer S, Sims S, Whitehead S, Wiley D, Beck S, Harrow JL.

Database (Oxford). 2013 Apr 15;2013:bat011. doi: 10.1093/database/bat011.


The YARHG domain: an extracellular domain in search of a function.

Coggill P, Bateman A.

PLoS One. 2012;7(5):e35575. doi: 10.1371/journal.pone.0035575.


The Pfam protein families database.

Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD.

Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301. doi: 10.1093/nar/gkr1065.


InterPro in 2011: new developments in the family and domain prediction database.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY.

Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12. doi: 10.1093/nar/gkr948.


The tammar wallaby major histocompatibility complex shows evidence of past genomic instability.

Siddle HV, Deakin JE, Coggill P, Whilming LG, Harrow J, Kaufman J, Beck S, Belov K.

BMC Genomics. 2011 Aug 19;12:421. doi: 10.1186/1471-2164-12-421.


DUFs: families in search of function.

Bateman A, Coggill P, Finn RD.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1148-52. doi: 10.1107/S1744309110001685.


The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes.

Chang C, Coggill P, Bateman A, Finn RD, Cymborowski M, Otwinowski Z, Minor W, Volkart L, Joachimiak A.

BMC Struct Biol. 2009 Dec 17;9:75. doi: 10.1186/1472-6807-9-75.


The Pfam protein families database.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985.


A novel system of polymorphic and diverse NK cell receptors in primates.

Averdam A, Petersen B, Rosner C, Neff J, Roos C, Eberle M, Aujard F, M√ľnch C, Schempp W, Carrington M, Shiina T, Inoko H, Knaust F, Coggill P, Sehra H, Beck S, Abi-Rached L, Reinhardt R, Walter L.

PLoS Genet. 2009 Oct;5(10):e1000688. doi: 10.1371/journal.pgen.1000688.


MHC-linked and un-linked class I genes in the wallaby.

Siddle HV, Deakin JE, Coggill P, Hart E, Cheng Y, Wong ES, Harrow J, Beck S, Belov K.

BMC Genomics. 2009 Jul 14;10:310. doi: 10.1186/1471-2164-10-310.


A common variant associated with dyslexia reduces expression of the KIAA0319 gene.

Dennis MY, Paracchini S, Scerri TS, Prokunina-Olsson L, Knight JC, Wade-Martins R, Coggill P, Beck S, Green ED, Monaco AP.

PLoS Genet. 2009 Mar;5(3):e1000436. doi: 10.1371/journal.pgen.1000436.

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