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Items: 15

1.

Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins.

Zanzoni A, Spinelli L, Braham S, Brun C.

Microbiome. 2017 Aug 10;5(1):89. doi: 10.1186/s40168-017-0307-1.

2.

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.

3.

SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks.

Olorin E, O'Brien KT, Palopoli N, Pérez-Bercoff Å, Shields DC, Edwards RJ.

F1000Res. 2015 Aug 5;4:477. doi: 10.12688/f1000research.6773.1. eCollection 2015.

4.

Redefining the BH3 Death Domain as a 'Short Linear Motif'.

Aouacheria A, Combet C, Tompa P, Hardwick JM.

Trends Biochem Sci. 2015 Dec;40(12):736-48. doi: 10.1016/j.tibs.2015.09.007. Epub 2015 Nov 3. Review.

5.

Multiple Weak Linear Motifs Enhance Recruitment and Processivity in SPOP-Mediated Substrate Ubiquitination.

Pierce WK, Grace CR, Lee J, Nourse A, Marzahn MR, Watson ER, High AA, Peng J, Schulman BA, Mittag T.

J Mol Biol. 2016 Mar 27;428(6):1256-1271. doi: 10.1016/j.jmb.2015.10.002. Epub 2015 Oct 22.

6.

QSLiMFinder: improved short linear motif prediction using specific query protein data.

Palopoli N, Lythgow KT, Edwards RJ.

Bioinformatics. 2015 Jul 15;31(14):2284-93. doi: 10.1093/bioinformatics/btv155. Epub 2015 Mar 19.

7.

The "histone mimicry" by pathogens.

Schaefer U, Ho JS, Prinjha RK, Tarakhovsky A.

Cold Spring Harb Symp Quant Biol. 2013;78:81-90. doi: 10.1101/sqb.2013.78.020339. Epub 2014 Apr 14.

8.

3did: a catalog of domain-based interactions of known three-dimensional structure.

Mosca R, Céol A, Stein A, Olivella R, Aloy P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D374-9. doi: 10.1093/nar/gkt887. Epub 2013 Sep 29.

9.

SLiMScape: a protein short linear motif analysis plugin for Cytoscape.

O'Brien KT, Haslam NJ, Shields DC.

BMC Bioinformatics. 2013 Jul 15;14:224. doi: 10.1186/1471-2105-14-224.

10.

Stereochemical determinants of C-terminal specificity in PDZ peptide-binding domains: a novel contribution of the carboxylate-binding loop.

Amacher JF, Cushing PR, Bahl CD, Beck T, Madden DR.

J Biol Chem. 2013 Feb 15;288(7):5114-26. doi: 10.1074/jbc.M112.401588. Epub 2012 Dec 15.

11.

Secondary structure, a missing component of sequence-based minimotif definitions.

Sargeant DP, Gryk MR, Maciejewski MW, Thapar V, Kundeti V, Rajasekaran S, Romero P, Dunker K, Li SC, Kaneko T, Schiller MR.

PLoS One. 2012;7(12):e49957. doi: 10.1371/journal.pone.0049957. Epub 2012 Dec 7.

12.

Disordered binding regions and linear motifs--bridging the gap between two models of molecular recognition.

Mészáros B, Dosztányi Z, Simon I.

PLoS One. 2012;7(10):e46829. doi: 10.1371/journal.pone.0046829. Epub 2012 Oct 3.

13.

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions.

Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ, Edwards RJ.

Nucleic Acids Res. 2012 Nov;40(21):10628-41. doi: 10.1093/nar/gks854. Epub 2012 Sep 12.

14.
15.

ELM--the database of eukaryotic linear motifs.

Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, Jehl P, McGuigan C, Dymecka M, Chica C, Luck K, Via A, Chatr-Aryamontri A, Haslam N, Grebnev G, Edwards RJ, Steinmetz MO, Meiselbach H, Diella F, Gibson TJ.

Nucleic Acids Res. 2012 Jan;40(Database issue):D242-51. doi: 10.1093/nar/gkr1064. Epub 2011 Nov 21.

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