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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
Direct NOE refinement of biomolecular structures using 2D NMR data.
Bonvin AM, Boelens R, Kaptein R. Bonvin AM, et al. J Biomol NMR. 1991 Sep;1(3):305-9. doi: 10.1007/BF01875523. J Biomol NMR. 1991. PMID: 1841701
Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations.
Bonvin AM, Vis H, Breg JN, Burgering MJ, Boelens R, Kaptein R. Bonvin AM, et al. J Mol Biol. 1994 Feb 11;236(1):328-41. doi: 10.1006/jmbi.1994.1138. J Mol Biol. 1994. PMID: 8107113
"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.
Bonvin AM, Rullmann JA, Lamerichs RM, Boelens R, Kaptein R. Bonvin AM, et al. Proteins. 1993 Apr;15(4):385-400. doi: 10.1002/prot.340150406. Proteins. 1993. PMID: 8460109
Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation.
Bonvin AM. Bonvin AM. Eur Biophys J. 2000;29(1):57-60. doi: 10.1007/s002490050251. Eur Biophys J. 2000. PMID: 10826779
Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.
Kalodimos CG, Bonvin AM, Salinas RK, Wechselberger R, Boelens R, Kaptein R. Kalodimos CG, et al. Among authors: bonvin am. EMBO J. 2002 Jun 17;21(12):2866-76. doi: 10.1093/emboj/cdf318. EMBO J. 2002. PMID: 12065400 Free PMC article.
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
Dominguez C, Boelens R, Bonvin AM. Dominguez C, et al. Among authors: bonvin am. J Am Chem Soc. 2003 Feb 19;125(7):1731-7. doi: 10.1021/ja026939x. J Am Chem Soc. 2003. PMID: 12580598
Use of very long-distance NOEs in a fully deuterated protein: an approach for rapid protein fold determination.
Koharudin LM, Bonvin AM, Kaptein R, Boelens R. Koharudin LM, et al. Among authors: bonvin am. J Magn Reson. 2003 Aug;163(2):228-35. doi: 10.1016/s1090-7807(03)00149-6. J Magn Reson. 2003. PMID: 12914838
Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.
Dominguez C, Bonvin AM, Winkler GS, van Schaik FM, Timmers HT, Boelens R. Dominguez C, et al. Among authors: bonvin am. Structure. 2004 Apr;12(4):633-44. doi: 10.1016/j.str.2004.03.004. Structure. 2004. PMID: 15062086
Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120.
Hsu ST, Bonvin AM. Hsu ST, et al. Among authors: bonvin am. Proteins. 2004 May 15;55(3):582-93. doi: 10.1002/prot.20061. Proteins. 2004. PMID: 15103622
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