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Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations.
Thukral L, Smith JC, Daidone I. Thukral L, et al. Among authors: daidone i. J Am Chem Soc. 2009 Dec 23;131(50):18147-52. doi: 10.1021/ja9064365. J Am Chem Soc. 2009. PMID: 19919102
New insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide.
Zanetti Polzi L, Amadei A, Aschi M, Daidone I. Zanetti Polzi L, et al. Among authors: daidone i. J Am Chem Soc. 2011 Aug 3;133(30):11414-7. doi: 10.1021/ja2028662. Epub 2011 Jul 8. J Am Chem Soc. 2011. PMID: 21692535
The PMM/MD approach allows isolation of the amide I' signal arising from any desired peptide group of the polypeptide chain and quantification of the effect of the excitonic coupling on the frequency position. ...In addition, our data show that a red shift of the amide …
The PMM/MD approach allows isolation of the amide I' signal arising from any desired peptide group of the polypeptide chain and quant …
Theoretical characterization of alpha-helix and beta-hairpin folding kinetics.
Daidone I, D'Abramo M, Di Nola A, Amadei A. Daidone I, et al. J Am Chem Soc. 2005 Oct 26;127(42):14825-32. doi: 10.1021/ja053383f. J Am Chem Soc. 2005. PMID: 16231936
Aggregation of small peptides studied by molecular dynamics simulations.
Flöck D, Rossetti G, Daidone I, Amadei A, Di Nola A. Flöck D, et al. Among authors: daidone i. Proteins. 2006 Dec 1;65(4):914-21. doi: 10.1002/prot.21168. Proteins. 2006. PMID: 16981204
Mechanism of DNA recognition by the restriction enzyme EcoRV.
Zahran M, Daidone I, Smith JC, Imhof P. Zahran M, et al. Among authors: daidone i. J Mol Biol. 2010 Aug 20;401(3):415-32. doi: 10.1016/j.jmb.2010.06.026. Epub 2010 Jun 18. J Mol Biol. 2010. PMID: 20600128
Configurational subdiffusion of peptides: a network study.
Neusius T, Daidone I, Sokolov IM, Smith JC. Neusius T, et al. Among authors: daidone i. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Feb;83(2 Pt 1):021902. doi: 10.1103/PhysRevE.83.021902. Epub 2011 Feb 2. Phys Rev E Stat Nonlin Soft Matter Phys. 2011. PMID: 21405858
Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains.
Daidone I, Neuweiler H, Doose S, Sauer M, Smith JC. Daidone I, et al. PLoS Comput Biol. 2010 Jan 22;6(1):e1000645. doi: 10.1371/journal.pcbi.1000645. PLoS Comput Biol. 2010. PMID: 20098498 Free PMC article.
Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation.
Noé F, Daidone I, Smith JC, di Nola A, Amadei A. Noé F, et al. Among authors: daidone i. J Phys Chem B. 2008 Sep 4;112(35):11155-63. doi: 10.1021/jp801391t. Epub 2008 Aug 12. J Phys Chem B. 2008. PMID: 18698708
Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding.
Daidone I, Ulmschneider MB, Di Nola A, Amadei A, Smith JC. Daidone I, et al. Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15230-5. doi: 10.1073/pnas.0701401104. Epub 2007 Sep 19. Proc Natl Acad Sci U S A. 2007. PMID: 17881585 Free PMC article.
Subdiffusion in peptides originates from the fractal-like structure of configuration space.
Neusius T, Daidone I, Sokolov IM, Smith JC. Neusius T, et al. Among authors: daidone i. Phys Rev Lett. 2008 May 9;100(18):188103. doi: 10.1103/PhysRevLett.100.188103. Epub 2008 May 6. Phys Rev Lett. 2008. PMID: 18518418
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