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Results: 17

1.

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.

PMID:
24655206
[PubMed - in process]
2.

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.

PMID:
23526684
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
22984947
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
22812654
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22809338
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
22544766
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
21354429
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
20969427
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
19237445
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
18515374
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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

Ruvinsky AM, Vakser IA.

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

PMID:
17910068
[PubMed - indexed for MEDLINE]
12.

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
[PubMed - indexed for MEDLINE]
13.
14.

Novel statistical-thermodynamic methods to predict protein-ligand binding positions using probability distribution functions.

Ruvinsky AM, Kozintsev AV.

Proteins. 2006 Jan 1;62(1):202-8.

PMID:
16287127
[PubMed - indexed for MEDLINE]
15.

New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy.

Ruvinsky AM, Kozintsev AV.

J Comput Chem. 2005 Aug;26(11):1089-95.

PMID:
15929088
[PubMed - indexed for MEDLINE]
16.

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
[PubMed - indexed for MEDLINE]
17.

The key role of atom types, reference states, and interaction cutoff radii in the knowledge-based method: new variational approach.

Ruvinsky AM, Kozintsev AV.

Proteins. 2005 Mar 1;58(4):845-51.

PMID:
15651026
[PubMed - indexed for MEDLINE]

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