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Items: 18

1.

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.

PMID:
28188534
2.

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.

3.

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.

4.

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.

5.

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.

6.

Nucleotide binding database NBDB--a collection of sequence motifs with specific protein-ligand interactions.

Zheng Z, Goncearenco A, Berezovsky IN.

Nucleic Acids Res. 2016 Jan 4;44(D1):D301-7. doi: 10.1093/nar/gkv1124.

7.

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.

8.

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
9.

Protein function from its emergence to diversity in contemporary proteins.

Goncearenco A, Berezovsky IN.

Phys Biol. 2015 Jun 9;12(4):045002. doi: 10.1088/1478-3975/12/4/045002.

PMID:
26057563
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. Review.

12.

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins.

Goncearenco A, Ma BG, Berezovsky IN.

Nucleic Acids Res. 2014 Mar;42(5):2879-92. doi: 10.1093/nar/gkt1336.

13.

SPACER: Server for predicting allosteric communication and effects of regulation.

Goncearenco A, Mitternacht S, Yong T, Eisenhaber B, Eisenhaber F, Berezovsky IN.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W266-72. doi: 10.1093/nar/gkt460.

14.

A dominant negative heterozygous G87R mutation in the zinc transporter, ZnT-2 (SLC30A2), results in transient neonatal zinc deficiency.

Lasry I, Seo YA, Ityel H, Shalva N, Pode-Shakked B, Glaser F, Berman B, Berezovsky I, Goncearenco A, Klar A, Levy J, Anikster Y, Kelleher SL, Assaraf YG.

J Biol Chem. 2012 Aug 24;287(35):29348-61. doi: 10.1074/jbc.M112.368159.

15.

Exploring the evolution of protein function in Archaea.

Goncearenco A, Berezovsky IN.

BMC Evol Biol. 2012 May 30;12:75.

16.

Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins.

Goncearenco A, Berezovsky IN.

Bioinformatics. 2011 Sep 1;27(17):2368-75. doi: 10.1093/bioinformatics/btr396.

PMID:
21724592
17.

Prototypes of elementary functional loops unravel evolutionary connections between protein functions.

Goncearenco A, Berezovsky IN.

Bioinformatics. 2010 Sep 15;26(18):i497-503. doi: 10.1093/bioinformatics/btq374.

18.

Thermophilic adaptation of protein complexes inferred from proteomic homology modeling.

Ma BG, Goncearenco A, Berezovsky IN.

Structure. 2010 Jul 14;18(7):819-28. doi: 10.1016/j.str.2010.04.004.

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