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Results: 1 to 20 of 58

1.

Protein models docking benchmark 2.

Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA.

Proteins. 2015 May;83(5):891-7. doi: 10.1002/prot.24784. Epub 2015 Mar 25.

2.

Structural templates for comparative protein docking.

Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA.

Proteins. 2014 Dec 9. doi: 10.1002/prot.24736. [Epub ahead of print]

PMID:
25488330
3.

Protein-protein docking: from interaction to interactome.

Vakser IA.

Biophys J. 2014 Oct 21;107(8):1785-93. doi: 10.1016/j.bpj.2014.08.033.

PMID:
25418159
4.

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.

5.

Blind prediction of interfacial water positions in CAPRI.

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ.

Proteins. 2014 Apr;82(4):620-32. doi: 10.1002/prot.24439. Epub 2013 Nov 23.

PMID:
24155158
6.

Structural templates for modeling homodimers.

Kundrotas PJ, Vakser IA, Janin J.

Protein Sci. 2013 Nov;22(11):1655-63. doi: 10.1002/pro.2361. Epub 2013 Sep 20.

7.

Global and local structural similarity in protein-protein complexes: implications for template-based docking.

Kundrotas PJ, Vakser IA.

Proteins. 2013 Dec;81(12):2137-42. doi: 10.1002/prot.24392. Epub 2013 Oct 17.

PMID:
23946125
8.

Protein models: the Grand Challenge of protein docking.

Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA.

Proteins. 2014 Feb;82(2):278-87. doi: 10.1002/prot.24385. Epub 2013 Oct 17.

PMID:
23934791
9.

Protein-protein alternative binding modes do not overlap.

Kundrotas PJ, Vakser IA.

Protein Sci. 2013 Aug;22(8):1141-5. doi: 10.1002/pro.2295. Epub 2013 Jul 3.

10.

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.

11.

Low-resolution structural modeling of protein interactome.

Vakser IA.

Curr Opin Struct Biol. 2013 Apr;23(2):198-205. doi: 10.1016/j.sbi.2012.12.003. Epub 2013 Jan 5. Review.

12.

GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions.

Kundrotas PJ, Zhu Z, Vakser IA.

Hum Genomics. 2012 Jul 11;6(1):7. doi: 10.1186/1479-7364-6-7. Review.

13.

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.

14.

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.

15.

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.

16.

Templates are available to model nearly all complexes of structurally characterized proteins.

Kundrotas PJ, Zhu Z, Janin J, Vakser IA.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9438-41. doi: 10.1073/pnas.1200678109. Epub 2012 May 29.

17.

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.

18.

Protein docking by the interface structure similarity: how much structure is needed?

Sinha R, Kundrotas PJ, Vakser IA.

PLoS One. 2012;7(2):e31349. doi: 10.1371/journal.pone.0031349. Epub 2012 Feb 13.

19.

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking.

Liu S, Vakser IA.

BMC Bioinformatics. 2011 Jul 11;12:280. doi: 10.1186/1471-2105-12-280.

20.

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.

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