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Results: 1 to 20 of 55

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.

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
[PubMed - in process]
3.

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.

PMID:
23996787
[PubMed - indexed for MEDLINE]
4.

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
[PubMed - indexed for MEDLINE]
5.

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
[PubMed - indexed for MEDLINE]
6.

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.

PMID:
23775945
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

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.

PMID:
23294579
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23245398
[PubMed - in process]
Free PMC Article
10.

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
11.

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
12.

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
13.

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.

PMID:
22645367
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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
15.

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.

PMID:
22348074
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
21745398
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
18.

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
19.

Docking by structural similarity at protein-protein interfaces.

Sinha R, Kundrotas PJ, Vakser IA.

Proteins. 2010 Nov 15;78(15):3235-41. doi: 10.1002/prot.22812.

PMID:
20715056
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Accuracy of protein-protein binding sites in high-throughput template-based modeling.

Kundrotas PJ, Vakser IA.

PLoS Comput Biol. 2010 Apr 1;6(4):e1000727. doi: 10.1371/journal.pcbi.1000727.

PMID:
20369011
[PubMed - indexed for MEDLINE]
Free PMC Article

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