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Items: 1 to 20 of 95

1.

Predicting binding within disordered protein regions to structurally characterised peptide-binding domains.

Khan W, Duffy F, Pollastri G, Shields DC, Mooney C.

PLoS One. 2013 Sep 3;8(9):e72838. doi: 10.1371/journal.pone.0072838. eCollection 2013.

2.

Intrinsic disorder in the Protein Data Bank.

Le Gall T, Romero PR, Cortese MS, Uversky VN, Dunker AK.

J Biomol Struct Dyn. 2007 Feb;24(4):325-42.

PMID:
17206849
3.

Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome.

Davey NE, Seo MH, Yadav VK, Jeon J, Nim S, Krystkowiak I, Blikstad C, Dong D, Markova N, Kim PM, Ivarsson Y.

FEBS J. 2017 Feb;284(3):485-498. doi: 10.1111/febs.13995. Epub 2017 Jan 18.

4.

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
5.

A benchmark testing ground for integrating homology modeling and protein docking.

Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D.

Proteins. 2017 Jan;85(1):10-16. doi: 10.1002/prot.25063. Epub 2016 Nov 13.

6.

Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how.

London N, Raveh B, Schueler-Furman O.

Curr Opin Struct Biol. 2013 Dec;23(6):894-902. doi: 10.1016/j.sbi.2013.07.006. Epub 2013 Oct 15. Review.

PMID:
24138780
7.

The unfoldomics decade: an update on intrinsically disordered proteins.

Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN.

BMC Genomics. 2008 Sep 16;9 Suppl 2:S1. doi: 10.1186/1471-2164-9-S2-S1.

8.

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.

Kurcinski M, Jamroz M, Blaszczyk M, Kolinski A, Kmiecik S.

Nucleic Acids Res. 2015 Jul 1;43(W1):W419-24. doi: 10.1093/nar/gkv456. Epub 2015 May 5.

9.

SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method.

Zhang T, Faraggi E, Xue B, Dunker AK, Uversky VN, Zhou Y.

J Biomol Struct Dyn. 2012;29(4):799-813.

10.

Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power.

Wang Z, Sun H, Yao X, Li D, Xu L, Li Y, Tian S, Hou T.

Phys Chem Chem Phys. 2016 May 14;18(18):12964-75. doi: 10.1039/c6cp01555g. Epub 2016 Apr 25.

PMID:
27108770
11.

Computational analysis of interactions in structurally available protein-glycosaminoglycan complexes.

Samsonov SA, Pisabarro MT.

Glycobiology. 2016 Aug;26(8):850-861. doi: 10.1093/glycob/cww055. Epub 2016 Jun 24.

PMID:
27496767
12.
13.

Transient protein-protein interface prediction: datasets, features, algorithms, and the RAD-T predictor.

Bendell CJ, Liu S, Aumentado-Armstrong T, Istrate B, Cernek PT, Khan S, Picioreanu S, Zhao M, Murgita RA.

BMC Bioinformatics. 2014 Mar 24;15:82. doi: 10.1186/1471-2105-15-82.

14.

Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures.

Stein A, Aloy P.

PLoS Comput Biol. 2010 May 20;6(5):e1000789. doi: 10.1371/journal.pcbi.1000789.

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.

Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction.

Yan C, Xu X, Zou X.

Structure. 2016 Oct 4;24(10):1842-1853. doi: 10.1016/j.str.2016.07.021. Epub 2016 Sep 15.

17.

A fragment-based docking simulation for investigating peptide-protein bindings.

Liao JM, Wang YT, Lin CS.

Phys Chem Chem Phys. 2017 Apr 19;19(16):10436-10442. doi: 10.1039/c6cp07136h.

PMID:
28379224
18.

Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource.

Kirys T, Ruvinsky AM, Singla D, Tuzikov AV, Kundrotas PJ, Vakser IA.

BMC Bioinformatics. 2015 Jul 31;16:243. doi: 10.1186/s12859-015-0672-3.

19.

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.

Ravindranath PA, Forli S, Goodsell DS, Olson AJ, Sanner MF.

PLoS Comput Biol. 2015 Dec 2;11(12):e1004586. doi: 10.1371/journal.pcbi.1004586. eCollection 2015 Dec.

20.

The scoring bias in reverse docking and the score normalization strategy to improve success rate of target fishing.

Luo Q, Zhao L, Hu J, Jin H, Liu Z, Zhang L.

PLoS One. 2017 Feb 14;12(2):e0171433. doi: 10.1371/journal.pone.0171433. eCollection 2017.

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