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Results: 1 to 20 of 33

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.

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
4.

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.

5.

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
6.

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
7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

GWIDD: Genome-wide protein docking database.

Kundrotas PJ, Zhu Z, Vakser IA.

Nucleic Acids Res. 2010 Jan;38(Database issue):D513-7. doi: 10.1093/nar/gkp944. Epub 2009 Nov 9.

14.

Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.

Kundrotas PJ, Lensink MF, Alexov E.

Int J Biol Macromol. 2008 Aug 15;43(2):198-208. doi: 10.1016/j.ijbiomac.2008.05.004. Epub 2008 May 21.

PMID:
18572239
15.

Predicting 3D structures of protein-protein complexes.

Vakser IA, Kundrotas P.

Curr Pharm Biotechnol. 2008 Apr;9(2):57-66. Review.

PMID:
18393862
16.

On the electrostatic component of protein-protein binding free energy.

Talley K, Ng C, Shoppell M, Kundrotas P, Alexov E.

PMC Biophys. 2008 Nov 5;1(1):2. doi: 10.1186/1757-5036-1-2.

17.

Predicting interacting and interfacial residues using continuous sequence segments.

Kundrotas P, Alexov E.

Int J Biol Macromol. 2007 Dec 1;41(5):615-23. Epub 2007 Aug 9.

PMID:
17850859
18.

Optimization of electrostatic interactions in protein-protein complexes.

Brock K, Talley K, Coley K, Kundrotas P, Alexov E.

Biophys J. 2007 Nov 15;93(10):3340-52. Epub 2007 Aug 10.

19.

Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families.

Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E.

J Bioinform Comput Biol. 2007 Jun;5(3):693-715.

PMID:
17688312
20.

BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families.

Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E.

Int J Biol Macromol. 2007 Jun 1;41(1):114-9. Epub 2007 Jan 25.

PMID:
17320167
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