Browsing by Subject "Amino acids"
Now showing items 1-11 of 11
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Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations
(2011)Peptide and protein self-assembly is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. Sequence repeats from self-assembling ...
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Amyloid-like self-assembly of peptide sequences from the adenovirus fiber shaft: Insights from molecular dynamics simulations
(2009)The self-assembly of peptides and proteins into nanostructures is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. ...
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Computational protein design: The proteus software and selected applications
(2013)We describe an automated procedure for protein design, implemented in a flexible software package, called Proteus. System setup and calculation of an energy matrix are done with the XPLOR modeling program and its sophisticated ...
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Article
Direct detection of Fe(IV)=O intermediates in the cytochrome aa3 oxidase from Paracoccus denitrificans[H2O2 reaction
(2003)We report the first evidence for the formation of the "607- and 580-nm forms" in the cytochrome oxidase aa3/H2O2 reaction without the involvement of tyrosine 280. The pKa of the 607-580-nm transition is 7.5. The 607-nm ...
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Article
Helix formation by alanine-based peptides in pure water and electrolyte solutions: Insights from molecular dynamics simulations
(2013)Specific ion effects on oligopeptide conformations in solution are attracting strong research attention, because of their impact on the protein-folding problem and on several important biological-biotechnological applications. ...
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Article
Helix formation by alanine-based peptides in pure water and electrolyte solutions: Insights from molecular dynamics simulationsAAA
(2013)Specific ion effects on oligopeptide conformations in solution are attracting strong research attention, because of their impact on the protein-folding problem and on several important biological-biotechnological applications. ...
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Ionic liquids for the molecular enantiorecognition of free l-T3, l-T4 and d-T4
(2015)Ionic liquids were proposed for the molecular enantiorecognition of free l-T3, l-T4 and d-T4. l-Phenylalanine tert-butyl ester lactate (l-PheC4-Lac), l-alanine tert-butyl ester l-lactate (l-AlaC4-Lac) and l-alanine tert-butyl ...
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Protein secondary structure prediction with bidirectional recurrent neural nets: Can weight updating for each residue enhance performance?
(2010)Successful protein secondary structure prediction is an important step towards modelling protein 3D structure, with several practical applications. Even though in the last four decades several PSSP algorithms have been ...
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A residue-pairwise generalized born scheme suitable for protein design calculations
(2005)We describe an efficient generalized Born (GB) approximation for proteins, in which the interaction energy between two amino acids depends on the whole protein structure, but can be accurately computed from residue-pairwise ...
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Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: Insights from molecular dynamics
(2011)We examine computationally the dipeptide and tetrapeptide of alanine in pure water and solutions of sodium chloride (NaCl) and iodide (NaI), with salt concentrations up to 3 M. Enhanced sampling of the configuration space ...
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Article
Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: Insights from molecular dynamicsAAA
(2011)We examine computationally the dipeptide and tetrapeptide of alanine in pure water and solutions of sodium chloride (NaCl) and iodide (NaI), with salt concentrations up to 3 M. Enhanced sampling of the configuration space ...