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Items: 1 to 20 of 40

1.

Yeast protein-protein interaction binding sites: prediction from the motif-motif, motif-domain and domain-domain levels.

Pang E, Lin K.

Mol Biosyst. 2010 Nov;6(11):2164-73. doi: 10.1039/c0mb00038h. Epub 2010 Aug 17.

PMID:
20714642
2.
3.

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. Epub 2009 Nov 17.

4.

SMART 6: recent updates and new developments.

Letunic I, Doerks T, Bork P.

Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32. doi: 10.1093/nar/gkn808. Epub 2008 Oct 31.

5.

InterPro: the integrative protein signature database.

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. doi: 10.1093/nar/gkn785. Epub 2008 Oct 21.

6.

Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences.

Pitre S, North C, Alamgir M, Jessulat M, Chan A, Luo X, Green JR, Dumontier M, Dehne F, Golshani A.

Nucleic Acids Res. 2008 Aug;36(13):4286-94. doi: 10.1093/nar/gkn390. Epub 2008 Jun 27.

7.

Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences.

Guo Y, Yu L, Wen Z, Li M.

Nucleic Acids Res. 2008 May;36(9):3025-30. doi: 10.1093/nar/gkn159. Epub 2008 Apr 4.

8.

Recent progress and future directions in protein-protein docking.

Ritchie DW.

Curr Protein Pept Sci. 2008 Feb;9(1):1-15. Review.

PMID:
18336319
9.

Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset.

Guo J, Wu X, Zhang DY, Lin K.

Nucleic Acids Res. 2008 Apr;36(6):2002-11. doi: 10.1093/nar/gkn016. Epub 2008 Feb 14.

10.

The BioGRID Interaction Database: 2008 update.

Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40. Epub 2007 Nov 13.

11.

DOMINE: a database of protein domain interactions.

Raghavachari B, Tasneem A, Przytycka TM, Jothi R.

Nucleic Acids Res. 2008 Jan;36(Database issue):D656-61. Epub 2007 Oct 2.

12.
13.

Predicting protein-protein interactions based only on sequences information.

Shen J, Zhang J, Luo X, Zhu W, Yu K, Chen K, Li Y, Jiang H.

Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4337-41. Epub 2007 Mar 5.

14.

Protein-protein interaction site prediction based on conditional random fields.

Li MH, Lin L, Wang XL, Liu T.

Bioinformatics. 2007 Mar 1;23(5):597-604. Epub 2007 Jan 18.

PMID:
17234636
15.

DOMINO: a database of domain-peptide interactions.

Ceol A, Chatr-aryamontri A, Santonico E, Sacco R, Castagnoli L, Cesareni G.

Nucleic Acids Res. 2007 Jan;35(Database issue):D557-60. Epub 2006 Nov 29.

16.

Predicting domain-domain interactions using a parsimony approach.

Guimarães KS, Jothi R, Zotenko E, Przytycka TM.

Genome Biol. 2006;7(11):R104.

17.

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.

Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A.

BMC Bioinformatics. 2006 Jul 27;7:365.

18.

An integrated approach to the prediction of domain-domain interactions.

Lee H, Deng M, Sun F, Chen T.

BMC Bioinformatics. 2006 May 25;7:269.

19.

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF.

Nature. 2006 Mar 30;440(7084):637-43. Epub 2006 Mar 22.

PMID:
16554755
20.

A unique set of SH3-SH3 interactions controls IB1 homodimerization.

Kristensen O, Guenat S, Dar I, Allaman-Pillet N, Abderrahmani A, Ferdaoussi M, Roduit R, Maurer F, Beckmann JS, Kastrup JS, Gajhede M, Bonny C.

EMBO J. 2006 Feb 22;25(4):785-97. Epub 2006 Feb 2.

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