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Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations.
Thukral L, Daidone I, Smith JC. Thukral L, et al. Among authors: daidone i. PLoS Comput Biol. 2011 Sep;7(9):e1002137. doi: 10.1371/journal.pcbi.1002137. Epub 2011 Sep 8. PLoS Comput Biol. 2011. PMID: 21931542 Free PMC article.
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.
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
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
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments.
Noé F, Doose S, Daidone I, Löllmann M, Sauer M, Chodera JD, Smith JC. Noé F, et al. Among authors: daidone i. Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4822-7. doi: 10.1073/pnas.1004646108. Epub 2011 Mar 2. Proc Natl Acad Sci U S A. 2011. PMID: 21368203 Free PMC article.
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