Thomas Simonson

Orcid: 0000-0002-5117-7338

According to our database1, Thomas Simonson authored at least 21 papers between 1999 and 2020.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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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

Simple models for nonpolar solvation: Parameterization and testing.
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

Computational protein design: The proteus software and selected applications.
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
A large decoy set of protein-protein complexes produced by flexible docking.
J. Comput. Chem., 2011

2010
Computational design of protein-ligand binding: Modifying the specificity of asparaginyl-tRNA synthetase.
J. Comput. Chem., 2010

A molecular mechanics model for imatinib and imatinib: kinase binding.
J. Comput. Chem., 2010

2009
Molecular mechanics models for tetracycline analogs.
J. Comput. Chem., 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
The tetracycline: Mg2+ complex: A molecular mechanics force field.
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


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