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Results: 1 to 20 of 43

1.

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.

PMID:
24371267
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
23737445
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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
[PubMed - indexed for MEDLINE]
4.

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
[PubMed - indexed for MEDLINE]
5.

Exploring the evolution of protein function in Archaea.

Goncearenco A, Berezovsky IN.

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

PMID:
22646318
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
22174669
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
21935347
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
21724592
[PubMed - indexed for MEDLINE]
Free Article
9.

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
[PubMed - indexed for MEDLINE]
10.

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.

PMID:
21159618
[PubMed - indexed for MEDLINE]
Free Article
11.

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
[PubMed - indexed for MEDLINE]
12.

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
[PubMed - indexed for MEDLINE]
13.

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.

PMID:
20823313
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
20637418
[PubMed - indexed for MEDLINE]
Free Article
15.

Do viral proteins possess unique biophysical features?

Tokuriki N, Oldfield CJ, Uversky VN, Berezovsky IN, Tawfik DS.

Trends Biochem Sci. 2009 Feb;34(2):53-9. doi: 10.1016/j.tibs.2008.10.009. Epub 2008 Dec 4.

PMID:
19062293
[PubMed - indexed for MEDLINE]
16.

Flowering buds of globular proteins: transpiring simplicity of protein organization.

Berezovsky IN, Trifonov EN.

Comp Funct Genomics. 2002;3(6):525-34. doi: 10.1002/cfg.223.

PMID:
18629251
[PubMed]
Free PMC Article
17.

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure.

Koczyk G, Berezovsky IN.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W239-45. doi: 10.1093/nar/gkn326. Epub 2008 May 23.

PMID:
18502776
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Positive and negative design in stability and thermal adaptation of natural proteins.

Berezovsky IN, Zeldovich KB, Shakhnovich EI.

PLoS Comput Biol. 2007 Mar 23;3(3):e52. Epub 2007 Feb 1.

PMID:
17381236
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Protein and DNA sequence determinants of thermophilic adaptation.

Zeldovich KB, Berezovsky IN, Shakhnovich EI.

PLoS Comput Biol. 2007 Jan 12;3(1):e5. Epub 2006 Nov 30.

PMID:
17222055
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Physical origins of protein superfamilies.

Zeldovich KB, Berezovsky IN, Shakhnovich EI.

J Mol Biol. 2006 Apr 7;357(4):1335-43. Epub 2006 Feb 6.

PMID:
16483605
[PubMed - indexed for MEDLINE]

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