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Items: 1 to 20 of 88


MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.

Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM.

Nucleic Acids Res. 2012 Mar;40(6):e47. doi: 10.1093/nar/gkr1294. Epub 2011 Dec 30.


Phage display selection of ligand residues important for Src homology 3 domain binding specificity.

Rickles RJ, Botfield MC, Zhou XM, Henry PA, Brugge JS, Zoller MJ.

Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):10909-13.


A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains.

Kundu K, Costa F, Backofen R.

Bioinformatics. 2013 Jul 1;29(13):i335-43. doi: 10.1093/bioinformatics/btt220.


Exhaustive search of linear information encoding protein-peptide recognition.

Kelil A, Dubreuil B, Levy ED, Michnick SW.

PLoS Comput Biol. 2017 Apr 20;13(4):e1005499. doi: 10.1371/journal.pcbi.1005499. eCollection 2017 Apr.


Why ligand cross-reactivity is high within peptide recognition domain families? A case study on human c-Src SH3 domain.

He P, Wu W, Wang HD, Liao KL, Zhang W, Lv FL, Yang K.

J Theor Biol. 2014 Jan 7;340:30-7. doi: 10.1016/j.jtbi.2013.08.026. Epub 2013 Sep 8.


Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data.

Kundu K, Costa F, Huber M, Reth M, Backofen R.

PLoS One. 2013 May 17;8(5):e62732. doi: 10.1371/journal.pone.0062732. Print 2013.


Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.

Andreatta M, Lund O, Nielsen M.

Bioinformatics. 2013 Jan 1;29(1):8-14. doi: 10.1093/bioinformatics/bts621. Epub 2012 Oct 24.


Efficient Identification of Murine M2 Macrophage Peptide Targeting Ligands by Phage Display and Next-Generation Sequencing.

Liu GW, Livesay BR, Kacherovsky NA, Cieslewicz M, Lutz E, Waalkes A, Jensen MC, Salipante SJ, Pun SH.

Bioconjug Chem. 2015 Aug 19;26(8):1811-7. doi: 10.1021/acs.bioconjchem.5b00344. Epub 2015 Jul 28.


Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets.

Krejci A, Hupp TR, Lexa M, Vojtesek B, Muller P.

Bioinformatics. 2016 Jan 1;32(1):9-16. doi: 10.1093/bioinformatics/btv522. Epub 2015 Sep 5.


Improving SH3 domain ligand selectivity using a non-natural scaffold.

Nguyen JT, Porter M, Amoui M, Miller WT, Zuckermann RN, Lim WA.

Chem Biol. 2000 Jul;7(7):463-73.


In vitro evolution of recognition specificity mediated by SH3 domains reveals target recognition rules.

Panni S, Dente L, Cesareni G.

J Biol Chem. 2002 Jun 14;277(24):21666-74. Epub 2002 Apr 19.


Decoding protein-protein interactions through combinatorial chemistry: sequence specificity of SHP-1, SHP-2, and SHIP SH2 domains.

Sweeney MC, Wavreille AS, Park J, Butchar JP, Tridandapani S, Pei D.

Biochemistry. 2005 Nov 15;44(45):14932-47.


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.


Insights into human Lck SH3 domain binding specificity: different binding modes of artificial and native ligands.

Tran T, Hoffmann S, Wiesehan K, Jonas E, Luge C, Aladag A, Willbold D.

Biochemistry. 2005 Nov 15;44(45):15042-52.


Unusual binding properties of the SH3 domain of the yeast actin-binding protein Abp1: structural and functional analysis.

Fazi B, Cope MJ, Douangamath A, Ferracuti S, Schirwitz K, Zucconi A, Drubin DG, Wilmanns M, Cesareni G, Castagnoli L.

J Biol Chem. 2002 Feb 15;277(7):5290-8. Epub 2001 Oct 19.


Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain.

Hou T, Chen K, McLaughlin WA, Lu B, Wang W.

PLoS Comput Biol. 2006 Jan;2(1):e1. Epub 2006 Jan 27.


The SH3 domains of endophilin and amphiphysin bind to the proline-rich region of synaptojanin 1 at distinct sites that display an unconventional binding specificity.

Cestra G, Castagnoli L, Dente L, Minenkova O, Petrelli A, Migone N, Hoffm├╝ller U, Schneider-Mergener J, Cesareni G.

J Biol Chem. 1999 Nov 5;274(45):32001-7.


Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCgamma, Crk, and Grb2.

Sparks AB, Rider JE, Hoffman NG, Fowlkes DM, Quillam LA, Kay BK.

Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1540-4.


The SH3 domain--a family of versatile peptide- and protein-recognition module.

Kaneko T, Li L, Li SS.

Front Biosci. 2008 May 1;13:4938-52. Review.


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