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Items: 1 to 20 of 310

1.

Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences.

Amos-Binks A, Patulea C, Pitre S, Schoenrock A, Gui Y, Green JR, Golshani A, Dehne F.

BMC Bioinformatics. 2011 Jun 2;12:225. doi: 10.1186/1471-2105-12-225.

2.

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.

3.

GAIA: a gram-based interaction analysis tool--an approach for identifying interacting domains in yeast.

Zhang KX, Ouellette BF.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S60. doi: 10.1186/1471-2105-10-S1-S60.

4.

Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale.

Li H, Li J, Wong L.

Bioinformatics. 2006 Apr 15;22(8):989-96. Epub 2006 Jan 29.

PMID:
16446278
5.

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
6.

Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811. Epub 2004 May 27.

PMID:
15166027
7.

Conserved network motifs allow protein-protein interaction prediction.

Albert I, Albert R.

Bioinformatics. 2004 Dec 12;20(18):3346-52. Epub 2004 Jul 9.

PMID:
15247093
8.

A correlated motif approach for finding short linear motifs from protein interaction networks.

Tan SH, Hugo W, Sung WK, Ng SK.

BMC Bioinformatics. 2006 Nov 16;7:502.

9.
10.

Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data.

Iqbal M, Freitas AA, Johnson CG, Vergassola M.

Bioinformatics. 2008 Sep 15;24(18):2064-70. doi: 10.1093/bioinformatics/btn366. Epub 2008 Jul 17.

PMID:
18641010
11.

Prediction of protein-protein interactions using random decision forest framework.

Chen XW, Liu M.

Bioinformatics. 2005 Dec 15;21(24):4394-400. Epub 2005 Oct 18.

PMID:
16234318
12.

A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.

Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G.

Science. 2002 Jan 11;295(5553):321-4. Epub 2001 Dec 13.

13.

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines.

González AJ, Liao L.

BMC Bioinformatics. 2010 Oct 29;11:537. doi: 10.1186/1471-2105-11-537.

14.

Prediction of short linear protein binding regions.

Mooney C, Pollastri G, Shields DC, Haslam NJ.

J Mol Biol. 2012 Jan 6;415(1):193-204. doi: 10.1016/j.jmb.2011.10.025. Epub 2011 Oct 21.

PMID:
22079048
15.

Domain-based small molecule binding site annotation.

Snyder KA, Feldman HJ, Dumontier M, Salama JJ, Hogue CW.

BMC Bioinformatics. 2006 Mar 17;7:152.

16.

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs.

Seitzer P, Wilbanks EG, Larsen DJ, Facciotti MT.

BMC Bioinformatics. 2012 Nov 27;13:317. doi: 10.1186/1471-2105-13-317.

17.

Accurate extraction of functional associations between proteins based on common interaction partners and common domains.

Okada K, Kanaya S, Asai K.

Bioinformatics. 2005 May 1;21(9):2043-8. Epub 2005 Feb 4.

PMID:
15699027
18.
19.

DAPID: a 3D-domain annotated protein-protein interaction database.

Chen YC, Chen HC, Yang JM.

Genome Inform. 2006;17(2):206-15.

PMID:
17503393
20.

Probabilistic prediction and ranking of human protein-protein interactions.

Scott MS, Barton GJ.

BMC Bioinformatics. 2007 Jul 5;8:239.

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