Thomas Simonson
Orcid: 0000-0002-5117-7338
According to our database1,
Thomas Simonson
authored at least 21 papers
between 1999 and 2020.
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Bibliography
2020
Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power.
PLoS Comput. Biol., 2020
2019
Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems.
J. Chem. Inf. Model., 2019
2017
Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design.
J. Comput. Chem., 2017
J. Comput. Chem., 2017
2016
Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic.
J. Comput. Chem., 2016
Protein: Ligand binding free energies: A stringent test for computational protein design.
J. Comput. Chem., 2016
2014
Pairwise decomposition of an MMGBSA energy function for computational protein design.
J. Comput. Chem., 2014
2013
Simulating GTP: Mg and GDP: Mg with a simple force field: A structural and thermodynamic analysis.
J. Comput. Chem., 2013
J. Comput. Chem., 2013
Monte carlo simulations of proteins at constant pH with generalized born solvent, flexible sidechains, and an effective dielectric boundary.
J. Comput. Chem., 2013
2011
J. Comput. Chem., 2011
2010
Computational design of protein-ligand binding: Modifying the specificity of asparaginyl-tRNA synthetase.
J. Comput. Chem., 2010
J. Comput. Chem., 2010
2009
2008
Computational protein design: Software implementation, parameter optimization, and performance of a simple model.
J. Comput. Chem., 2008
Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations.
BMC Bioinform., 2008
Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.
BMC Bioinform., 2008
2007
Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.
BMC Bioinform., 2007
2006
J. Comput. Chem., 2006
2001
Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges.
J. Comput. Chem., 2001
1999
Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect.
J. Comput. Chem., 1999