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Items: 1 to 20 of 36

1.

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.

Proteins. 2016 Apr 28. doi: 10.1002/prot.25007. [Epub ahead of print]

PMID:
27122118
2.

Text Mining for Protein Docking.

Badal VD, Kundrotas PJ, Vakser IA.

PLoS Comput Biol. 2015 Dec 9;11(12):e1004630. doi: 10.1371/journal.pcbi.1004630. eCollection 2015 Dec.

3.

Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource.

Kirys T, Ruvinsky AM, Singla D, Tuzikov AV, Kundrotas PJ, Vakser IA.

BMC Bioinformatics. 2015 Jul 31;16:243. doi: 10.1186/s12859-015-0672-3.

4.

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.

5.

Structural templates for comparative protein docking.

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

Proteins. 2015 Sep;83(9):1563-70. doi: 10.1002/prot.24736. Epub 2015 Jun 13.

PMID:
25488330
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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

Kundrotas PJ, Zhu Z, Vakser IA.

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

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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
18.

Predicting 3D structures of protein-protein complexes.

Vakser IA, Kundrotas P.

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

PMID:
18393862
19.

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.

20.

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
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