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Results: 1 to 20 of 31

1.

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]
2.

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]
3.

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]
4.

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 - in process]
5.

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
6.

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
7.

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
8.

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
9.

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
10.

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
11.

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.

PMID:
19900970
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
[PubMed - indexed for MEDLINE]
13.

Predicting 3D structures of protein-protein complexes.

Vakser IA, Kundrotas P.

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

PMID:
18393862
[PubMed - indexed for MEDLINE]
14.

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.

PMID:
19351424
[PubMed]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
17693468
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
[PubMed - indexed for MEDLINE]
18.

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
[PubMed - indexed for MEDLINE]
19.

Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives.

Kundrotas PJ, Alexov EG.

BMC Bioinformatics. 2006 Nov 16;7:503.

PMID:
17109752
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

PROTCOM: searchable database of protein complexes enhanced with domain-domain structures.

Kundrotas PJ, Alexov E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D575-9. Epub 2006 Oct 28.

PMID:
17071962
[PubMed - indexed for MEDLINE]
Free PMC Article

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