T
Thomas Simonson
Researcher at École Polytechnique
Publications - 134
Citations - 20961
Thomas Simonson is an academic researcher from École Polytechnique. The author has contributed to research in topics: Molecular dynamics & Protein design. The author has an hindex of 37, co-authored 130 publications receiving 20545 citations. Previous affiliations of Thomas Simonson include Howard Hughes Medical Institute & University of Cyprus.
Papers
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Journal ArticleDOI
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Axel T. Brunger,Axel T. Brunger,Paul D. Adams,G M Clore,W. L. DeLano,Piet Gros,R.W. Grosse-Kunstleve,R.W. Grosse-Kunstleve,Jiansheng Jiang,J. Kuszewski,Michael Nilges,Navraj S. Pannu,Randy J. Read,Luke M. Rice,Thomas Simonson,Gregory L. Warren +15 more
TL;DR: The Crystallography & NMR System (CNS) as mentioned in this paper is a software suite for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy.
Journal ArticleDOI
Implicit solvent models
Benoît Roux,Thomas Simonson +1 more
TL;DR: Implicit solvent models for biomolecular simulations are reviewed and their underlying statistical mechanical basis is discussed, and the relation between the solute fluctuations and its macroscopic dielectric constant(s) clarified.
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Free energy simulations come of age: protein-ligand recognition.
TL;DR: This work illustrates both molecular dynamics and Poisson-Boltzmann methods with a detailed study of amino acid recognition by aspartyl-tRNA synthetase, whose specificity is important for maintaining the integrity of the genetic code.
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Proton binding to proteins: pKa calculations with explicit and implicit solvent models
TL;DR: MDFE with a GB dielectric continuum solvent, used for the first time for pKa calculations, can describe protein reorganization accurately and gives encouraging agreement with experiment and with the explicit solvent simulations.
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Macromolecular electrostatics: continuum models and their growing pains.
TL;DR: Theoretical understanding of macromolecular electrostatics has advanced substantially over the past year, and Generalized Born and other techniques have led to the first molecular dynamics simulations of proteins and RNA with continuum solvent.