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Items: 1 to 20 of 50

1.

The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.

Eisenhaber B, Kuchibhatla D, Sherman W, Sirota FL, Berezovsky IN, Wong WC, Eisenhaber F.

Methods Mol Biol. 2016;1415:477-506. doi: 10.1007/978-1-4939-3572-7_25.

PMID:
27115649
2.

Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication.

Guarnera E, Berezovsky IN.

PLoS Comput Biol. 2016 Mar 3;12(3):e1004678. doi: 10.1371/journal.pcbi.1004678. eCollection 2016 Mar.

3.

Allosteric sites: remote control in regulation of protein activity.

Guarnera E, Berezovsky IN.

Curr Opin Struct Biol. 2016 Apr;37:1-8. doi: 10.1016/j.sbi.2015.10.004. Epub 2015 Nov 10. Review.

PMID:
26562539
4.

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. Epub 2015 Oct 26.

5.

Organization of the multiaminoacyl-tRNA synthetase complex and the cotranslational protein folding.

Berezovsky IN, Zheng Z, Kurotani A, Tokmakov AA, Kurochkin IV.

Protein Sci. 2015 Sep;24(9):1475-85. doi: 10.1002/pro.2735. Epub 2015 Jul 14.

PMID:
26131561
6.

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
8.

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. Epub 2013 Dec 25.

9.

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. Epub 2013 Jun 3.

10.

Unraveling hidden regulatory sites in structurally homologous metalloproteases.

Udi Y, Fragai M, Grossman M, Mitternacht S, Arad-Yellin R, Calderone V, Melikian M, Toccafondi M, Berezovsky IN, Luchinat C, Sagi I.

J Mol Biol. 2013 Jul 10;425(13):2330-46. doi: 10.1016/j.jmb.2013.04.009. Epub 2013 Apr 11.

PMID:
23583775
11.

Thermodynamics of allostery paves a way to allosteric drugs.

Berezovsky IN.

Biochim Biophys Acta. 2013 May;1834(5):830-5. doi: 10.1016/j.bbapap.2013.01.024. Epub 2013 Feb 1. Review.

PMID:
23376182
12.

Exploring the evolution of protein function in Archaea.

Goncearenco A, Berezovsky IN.

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

13.

Coherent conformational degrees of freedom as a structural basis for allosteric communication.

Mitternacht S, Berezovsky IN.

PLoS Comput Biol. 2011 Dec;7(12):e1002301. doi: 10.1371/journal.pcbi.1002301. Epub 2011 Dec 8.

14.

Binding leverage as a molecular basis for allosteric regulation.

Mitternacht S, Berezovsky IN.

PLoS Comput Biol. 2011 Sep;7(9):e1002148. doi: 10.1371/journal.pcbi.1002148. Epub 2011 Sep 15.

15.

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. Epub 2011 Jun 30.

16.

The diversity of physical forces and mechanisms in intermolecular interactions.

Berezovsky IN.

Phys Biol. 2011 Jun;8(3):035002. doi: 10.1088/1478-3975/8/3/035002. Epub 2011 May 13. Review.

PMID:
21572170
17.

A geometry-based generic predictor for catalytic and allosteric sites.

Mitternacht S, Berezovsky IN.

Protein Eng Des Sel. 2011 Apr;24(4):405-9. doi: 10.1093/protein/gzq115. Epub 2010 Dec 15.

18.

On the importance of amino acid sequence and spatial proximity of interacting residues for protein folding.

Mitternacht S, Berezovsky IN.

J Biomol Struct Dyn. 2011 Feb;28(4):607-9; discussion 669-674. No abstract available.

PMID:
21142232
19.

The MBLOSUM: a server for deriving mutation targets and position-specific substitution rates.

Ma BG, Berezovsky IN.

J Biomol Struct Dyn. 2010 Dec;28(3):415-9.

PMID:
20919756
20.

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.

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