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Items: 1 to 20 of 71

1.

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 May 5. pii: gkw374. [Epub ahead of print]

2.

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.

3.

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):221-37. doi: 10.1016/j.jmb.2015.12.004. Epub 2015 Dec 14.

PMID:
26699921
4.

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.

PMID:
26676746
5.

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.

PMID:
26213149
6.

Editorial overview: Linking protein sequence and structural changes to function in the era of next-generation sequencing.

Panchenko AR, Babu MM.

Curr Opin Struct Biol. 2015 Jun;32:viii-x. doi: 10.1016/j.sbi.2015.06.005. No abstract available.

PMID:
26199202
7.

6 Combined influence of linker DNA and histone tails on nucleosome dynamics as revealed by microsecond molecular dynamics simulations.

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

J Biomol Struct Dyn. 2015;33 Suppl 1:3. doi: 10.1080/07391102.2015.1032630. No abstract available.

PMID:
26103217
8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization.

Nishi H, Hashimoto K, Madej T, Panchenko AR.

Prog Mol Biol Transl Sci. 2013;117:3-24. doi: 10.1016/B978-0-12-386931-9.00001-5. Review.

18.

Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes.

Nishi H, Fong JH, Chang C, Teichmann SA, Panchenko AR.

Mol Biosyst. 2013 Jul;9(7):1620-6. doi: 10.1039/c3mb25514j. Epub 2013 Jan 30.

19.

Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases.

Hashimoto K, Rogozin IB, Panchenko AR.

Hum Mutat. 2012 Nov;33(11):1566-75. doi: 10.1002/humu.22145. Epub 2012 Jul 16.

20.

SPEER-SERVER: a web server for prediction of protein specificity determining sites.

Chakraborty A, Mandloi S, Lanczycki CJ, Panchenko AR, Chakrabarti S.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W242-8. doi: 10.1093/nar/gks559. Epub 2012 Jun 11.

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