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Items: 19

1.

Structural Insights Lead to a Negamycin Analogue with Improved Antimicrobial Activity against Gram-Negative Pathogens.

McKinney DC, Basarab GS, Cocozaki AI, Foulk MA, Miller MD, Ruvinsky AM, Scott CW, Thakur K, Zhao L, Buurman ET, Narayan S.

ACS Med Chem Lett. 2015 Jul 12;6(8):930-5. doi: 10.1021/acsmedchemlett.5b00205. eCollection 2015 Aug 13.

2.

Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource.

Kirys T, Ruvinsky AM, Singla D, Tuzikov AV, Kundrotas PJ, Vakser IA.

BMC Bioinformatics. 2015 Jul 31;16:243. doi: 10.1186/s12859-015-0672-3.

3.

Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins.

Ruvinsky AM, Vakser IA, Rivera M.

J Chem Phys. 2014 Mar 21;140(11):115104. doi: 10.1063/1.4868229.

4.

Ensemble-based characterization of unbound and bound states on protein energy landscape.

Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA.

Protein Sci. 2013 Jun;22(6):734-44. doi: 10.1002/pro.2256. Epub 2013 Apr 29.

5.

Correlation analysis of the side-chains conformational distribution in bound and unbound proteins.

Kirys T, Ruvinsky AM, Tuzikov AV, Vakser IA.

BMC Bioinformatics. 2012 Sep 17;13:236. doi: 10.1186/1471-2105-13-236.

6.

The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin.

Yao H, Wang Y, Lovell S, Kumar R, Ruvinsky AM, Battaile KP, Vakser IA, Rivera M.

J Am Chem Soc. 2012 Aug 15;134(32):13470-81. doi: 10.1021/ja305180n. Epub 2012 Aug 1.

7.

Structure fluctuations and conformational changes in protein binding.

Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA.

J Bioinform Comput Biol. 2012 Apr;10(2):1241002. doi: 10.1142/S0219720012410028.

8.

Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.

Kirys T, Ruvinsky AM, Tuzikov AV, Vakser IA.

Proteins. 2012 Aug;80(8):2089-98. doi: 10.1002/prot.24103. Epub 2012 Jun 12.

9.

Side-chain conformational changes upon Protein-Protein Association.

Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA.

J Mol Biol. 2011 Apr 29;408(2):356-65. doi: 10.1016/j.jmb.2011.02.030. Epub 2011 Feb 25.

10.

Sequence composition and environment effects on residue fluctuations in protein structures.

Ruvinsky AM, Vakser IA.

J Chem Phys. 2010 Oct 21;133(15):155101. doi: 10.1063/1.3498743.

11.

The ruggedness of protein-protein energy landscape and the cutoff for 1/r(n) potentials.

Ruvinsky AM, Vakser IA.

Bioinformatics. 2009 May 1;25(9):1132-6. doi: 10.1093/bioinformatics/btp108. Epub 2009 Feb 23.

12.

Chasing funnels on protein-protein energy landscapes at different resolutions.

Ruvinsky AM, Vakser IA.

Biophys J. 2008 Sep;95(5):2150-9. doi: 10.1529/biophysj.108.132977. Epub 2008 May 30.

13.

Interaction cutoff effect on ruggedness of protein-protein energy landscape.

Ruvinsky AM, Vakser IA.

Proteins. 2008 Mar;70(4):1498-505.

PMID:
17910068
14.

Calculations of protein-ligand binding entropy of relative and overall molecular motions.

Ruvinsky AM.

J Comput Aided Mol Des. 2007 Jul;21(7):361-70. Epub 2007 May 15.

PMID:
17503189
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Novel knowledge-based potentials for ligand docking: variational approach to the old problem.

Ruvinsky AM, Kozintsev AV.

Biophys Chem. 2005 Apr 1;115(2-3):255-61. Epub 2004 Dec 23.

PMID:
15752615
19.
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