Bonvin AM - Search Results

1

Contacts-based prediction of binding affinity in protein-protein complexes.

Vangone A, Bonvin AM. Vangone A, et al. Among authors: bonvin am. Elife. 2015 Jul 20;4:e07454. doi: 10.7554/eLife.07454. Elife. 2015. PMID: 26193119 Free PMC article.

2

WHISCY: what information does surface conservation yield? Application to data-driven docking.

de Vries SJ, van Dijk AD, Bonvin AM. de Vries SJ, et al. Among authors: bonvin am. Proteins. 2006 May 15;63(3):479-89. doi: 10.1002/prot.20842. Proteins. 2006. PMID: 16450362

3

Intramolecular surface contacts contain information about protein-protein interface regions.

de Vries SJ, Bonvin AM. de Vries SJ, et al. Among authors: bonvin am. Bioinformatics. 2006 Sep 1;22(17):2094-8. doi: 10.1093/bioinformatics/btl275. Epub 2006 Jun 9. Bioinformatics. 2006. PMID: 16766554

4

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility.

van Dijk M, van Dijk AD, Hsu V, Boelens R, Bonvin AM. van Dijk M, et al. Among authors: bonvin am. Nucleic Acids Res. 2006 Jul 4;34(11):3317-25. doi: 10.1093/nar/gkl412. Print 2006. Nucleic Acids Res. 2006. PMID: 16820531 Free PMC article.

In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc. 125, 1731-1737] to explicitly deal with DNA flexibility. ...

In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. …

5

Modeling protein-protein complexes involved in the cytochrome C oxidase copper-delivery pathway.

van Dijk AD, Ciofi-Baffoni S, Banci L, Bertini I, Boelens R, Bonvin AM. van Dijk AD, et al. Among authors: bonvin am. J Proteome Res. 2007 Apr;6(4):1530-9. doi: 10.1021/pr060651f. Epub 2007 Mar 6. J Proteome Res. 2007. PMID: 17338559

6

How proteins get in touch: interface prediction in the study of biomolecular complexes.

de Vries SJ, Bonvin AM. de Vries SJ, et al. Among authors: bonvin am. Curr Protein Pept Sci. 2008 Aug;9(4):394-406. doi: 10.2174/138920308785132712. Curr Protein Pept Sci. 2008. PMID: 18691126

7

Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes.

Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AM, Kaptein R, Boelens R. Romanuka J, et al. Among authors: bonvin am. J Mol Biol. 2009 Jul 17;390(3):478-89. doi: 10.1016/j.jmb.2009.05.022. Epub 2009 May 18. J Mol Biol. 2009. PMID: 19450607

8

Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.

Karaca E, Melquiond AS, de Vries SJ, Kastritis PL, Bonvin AM. Karaca E, et al. Among authors: bonvin am. Mol Cell Proteomics. 2010 Aug;9(8):1784-94. doi: 10.1074/mcp.M000051-MCP201. Epub 2010 Mar 19. Mol Cell Proteomics. 2010. PMID: 20305088 Free PMC article.

9

Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark.

Kastritis PL, Bonvin AM. Kastritis PL, et al. Among authors: bonvin am. J Proteome Res. 2010 May 7;9(5):2216-25. doi: 10.1021/pr9009854. J Proteome Res. 2010. PMID: 20329755

10

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.

de Vries SJ, Melquiond AS, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JP, Bonvin AM. de Vries SJ, et al. Among authors: bonvin am. Proteins. 2010 Nov 15;78(15):3242-9. doi: 10.1002/prot.22814. Proteins. 2010. PMID: 20718048

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