Browsing by Author "Simonson, T."
Now showing items 1-13 of 13
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Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase
Archontis, Georgios Z.; Simonson, T.; Karplus, M. (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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Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase
Polydorides, Savvas; Amara, Najette; Aubard, C.; Plateau, P.; Simonson, T.; Archontis, Georgios Z. (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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Computational protein design: The proteus software and selected applications
Simonson, T.; Gaillard, T.; Mignon, D.; Schmidt Am Busch, M.; Lopes, A.; Amara, Najette; Polydorides, Savvas; Sedano, A.; Druart, Karen; Archontis, Georgios Z. (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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Computational sidechain placement and protein mutagenesis with implicit solvent models
Lopes, A.; Alexandrov, A.; Bathelt, C.; Archontis, Georgios Z.; Simonson, T. (2007)Structure prediction and computational protein design should benefit from accurate solvent models. We have applied implicit solvent models to two problems that are central to this area. First, we performed sidechain placement ...
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Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding
Simonson, T.; Archontis, Georgios Z.; Karplus, M. (1997)A method is proposed to include long-range electrostatic interactions in free energy calculations that involve the creation or deletion of net charges in a macromolecule. The vicinity of the mutation site is treated ...
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Dielectric relaxation in an enzyme active site: Molecular dynamics simulations interpreted with a macroscopic continuum model
Archontis, Georgios Z.; Simonson, T. (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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Free energy simulations come of age: Protein-ligand recognition
Simonson, T.; Archontis, Georgios Z.; Karplus, M. (2002)In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide ...
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A Poisson-Boltzmann Study of Charge Insertion in an Enzyme Active Site: The Effect of Dielectric Relaxation
Simonson, T.; Archontis, Georgios Z.; Karphis, M. (1999)Continuum solvent models are playing an increasing role in the study of aqueous solutions, particularly those involving protein solutes. To estimate the magnitude of dielectric relaxation and clarify the microscopic meaning ...
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Predicting the acid/base behavior of proteins: A constant-pH monte carlo approach with generalized born solvent
Aleksandrov, A.; Polydorides, Savvas; Archontis, Georgios Z.; Simonson, T. (2010)The acid/base properties of proteins are essential in biochemistry, and proton binding is a valuable reporter on electrostatic interactions. We propose a constant-pH Monte Carlo strategy to compute protonation free energies ...
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Proteus and the design of ligand binding sites
Polydorides, Savvas; Michael, E.; Mignon, D.; Druart, Karen; Archontis, Georgios Z.; Simonson, T. (2016)This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding ...
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Proton binding to proteins: A free-energy component analysis using a dielectric continuum model
Archontis, Georgios Z.; Simonson, T. (2005)Proton binding plays a critical role in protein structure and function. We report pKa calculations for three aspartates in two proteins, using a linear response approach, as well as a "standard" Poisson-Boltzmann approach. ...
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A residue-pairwise generalized born scheme suitable for protein design calculations
Archontis, Georgios Z.; Simonson, T. (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 amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations
Archontis, Georgios Z.; Simonson, T.; Moras, D.; Karplus, M. (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 ...