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Items: 1 to 20 of 67

1.

Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning.

Shaytan AK, Xiao H, Armeev GA, Wu C, Landsman D, Panchenko AR.

Nucleic Acids Res. 2017 Sep 19;45(16):9229-9243. doi: 10.1093/nar/gkx616.

2.

Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols.

Li M, Goncearenco A, Panchenko AR.

Methods Mol Biol. 2017;1550:235-260. doi: 10.1007/978-1-4939-6747-6_17.

3.

MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.

El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J.

Epigenetics Chromatin. 2017 Jan 10;10:2. doi: 10.1186/s13072-016-0109-x. eCollection 2017.

4.

Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers.

Rogozin IB, Lada AG, Goncearenco A, Green MR, De S, Nudelman G, Panchenko AR, Koonin EV, Pavlov YI.

Sci Rep. 2016 Dec 7;6:38133. doi: 10.1038/srep38133.

5.

Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response.

Biswas R, Gao S, Cultraro CM, Maity TK, Venugopalan A, Abdullaev Z, Shaytan AK, Carter CA, Thomas A, Rajan A, Song Y, Pitts S, Chen K, Bass S, Boland J, Hanada KI, Chen J, Meltzer PS, Panchenko AR, Yang JC, Pack S, Giaccone G, Schrump DS, Khan J, Guha U.

Cold Spring Harb Mol Case Stud. 2016 Nov;2(6):a001263.

6.

Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles.

Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR.

Data Brief. 2016 May 6;7:1678-81. doi: 10.1016/j.dib.2016.04.073. eCollection 2016 Jun.

7.

MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions.

Li M, Simonetti FL, Goncearenco A, Panchenko AR.

Nucleic Acids Res. 2016 Jul 8;44(W1):W494-501. doi: 10.1093/nar/gkw374. Epub 2016 May 5.

8.

HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants.

Draizen EJ, Shaytan AK, Mariño-Ramírez L, Talbert PB, Landsman D, Panchenko AR.

Database (Oxford). 2016 Mar 17;2016. pii: baw014. doi: 10.1093/database/baw014. Print 2016.

9.

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.

Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR.

J Mol Biol. 2016 Jan 16;428(1):221-237. doi: 10.1016/j.jmb.2015.12.004. Epub 2015 Dec 14.

10.

Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation.

Li M, Kales SC, Ma K, Shoemaker BA, Crespo-Barreto J, Cangelosi AL, Lipkowitz S, Panchenko AR.

Cancer Res. 2016 Feb 1;76(3):561-71. doi: 10.1158/0008-5472.CAN-14-3812. Epub 2015 Dec 16.

11.

Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.

Goncearenco A, Shaytan AK, Shoemaker BA, Panchenko AR.

Biophys J. 2015 Sep 15;109(6):1295-306. doi: 10.1016/j.bpj.2015.06.056. Epub 2015 Jul 23.

12.

Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers.

Shaytan AK, Landsman D, Panchenko AR.

Curr Opin Struct Biol. 2015 Jun;32:48-57. doi: 10.1016/j.sbi.2015.02.004. Epub 2015 Feb 27. Review.

13.

Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites.

Nishi H, Demir E, Panchenko AR.

J Mol Biol. 2015 Jan 30;427(2):511-20. doi: 10.1016/j.jmb.2014.11.001. Epub 2014 Nov 9.

14.

Physicochemical mechanisms of protein regulation by phosphorylation.

Nishi H, Shaytan A, Panchenko AR.

Front Genet. 2014 Aug 7;5:270. doi: 10.3389/fgene.2014.00270. eCollection 2014. Review.

15.

Coverage of protein domain families with structural protein-protein interactions: current progress and future trends.

Goncearenco A, Shoemaker BA, Zhang D, Sarychev A, Panchenko AR.

Prog Biophys Mol Biol. 2014 Nov-Dec;116(2-3):187-93. doi: 10.1016/j.pbiomolbio.2014.05.005. Epub 2014 Jun 13. Review.

16.

Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity.

Li M, Petukh M, Alexov E, Panchenko AR.

J Chem Theory Comput. 2014 Apr 8;10(4):1770-1780. Epub 2014 Feb 27.

17.

Computational large-scale mapping of protein-protein interactions using structural complexes.

Shoemaker B, Wuchty S, Panchenko AR.

Curr Protoc Protein Sci. 2013 Sep 24;73:Unit 3.9. doi: 10.1002/0471140864.ps0309s73.

18.

Molecular mechanisms of disease-causing missense mutations.

Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E.

J Mol Biol. 2013 Nov 1;425(21):3919-36. doi: 10.1016/j.jmb.2013.07.014. Epub 2013 Jul 16. Review.

19.

Cancer missense mutations alter binding properties of proteins and their interaction networks.

Nishi H, Tyagi M, Teng S, Shoemaker BA, Hashimoto K, Alexov E, Wuchty S, Panchenko AR.

PLoS One. 2013 Jun 14;8(6):e66273. doi: 10.1371/journal.pone.0066273. Print 2013.

20.

Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics.

Li M, Shoemaker BA, Thangudu RR, Ferraris JD, Burg MB, Panchenko AR.

J Phys Chem B. 2013 Oct 24;117(42):13226-34. doi: 10.1021/jp403310a. Epub 2013 Jun 25.

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