Browsing by Subject "Aspartate-tRNA Ligase"
Now showing items 1-5 of 5
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Article
Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase
(2001)Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to ...
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Article
Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase
(2011)Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a ...
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Article
Dielectric relaxation in an enzyme active site: Molecular dynamics simulations interpreted with a macroscopic continuum model
(2001)Dielectric relaxation plays an important role in many chemical processes in proteins, including acid-base titration, ligand binding, and charge transfer reactions. Its complexity makes experimental characterization difficult, ...
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Article
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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Article
Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations
(1998)Specific amino acid binding by aminoacyl-tRNA synthetases is necessary for correct translation of the genetic code. To obtain insight into the origin of the specificity, the binding to aspartyl-tRNA synthetase (AspRS) of ...