Thomas Simonson

Publication Activity (10 Years)

Years Active: 1999-2020
Publications (10 Years): 6

Top Topics

Stochastic Search Algorithms

Energy Function

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam, Thomas Simonson
Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power. PLoS Comput. Biol. 16 (1) (2020)
Antoine Charpentier, David Mignon, Sophie Barbe, Juan Cortés, Thomas Schiex, Thomas Simonson, David Allouche
Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems. J. Chem. Inf. Model. 59 (1) (2019)
Eleni Michael, Savvas Polydorides, Thomas Simonson, Georgios Archontis
Simple models for nonpolar solvation: Parameterization and testing. J. Comput. Chem. 38 (29) (2017)
Francesco Villa, David Mignon, Savvas Polydorides, Thomas Simonson
Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design. J. Comput. Chem. 38 (28) (2017)
David Mignon, Thomas Simonson
Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic. J. Comput. Chem. 37 (19) (2016)
Karen Druart, Zoltan Palmai, Eyaz Omarjee, Thomas Simonson
Protein: Ligand binding free energies: A stringent test for computational protein design. J. Comput. Chem. 37 (4) (2016)
Thomas Gaillard, Thomas Simonson
Pairwise decomposition of an MMGBSA energy function for computational protein design. J. Comput. Chem. 35 (18) (2014)
Thomas Simonson, Thomas Gaillard, David Mignon, Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Savvas Polydorides, Audrey Sedano, Karen Druart, Georgios Archontis
Computational protein design: The proteus software and selected applications. J. Comput. Chem. 34 (28) (2013)
Thomas Simonson, Priyadarshi Satpati
Simulating GTP: Mg and GDP: Mg with a simple force field: A structural and thermodynamic analysis. J. Comput. Chem. 34 (10) (2013)
Savvas Polydorides, Thomas Simonson
Monte carlo simulations of proteins at constant pH with generalized born solvent, flexible sidechains, and an effective dielectric boundary. J. Comput. Chem. 34 (31) (2013)
Guillaume Launay, Thomas Simonson
A large decoy set of protein-protein complexes produced by flexible docking. J. Comput. Chem. 32 (1) (2011)
Alexey Aleksandrov, Thomas Simonson
A molecular mechanics model for imatinib and imatinib: kinase binding. J. Comput. Chem. 31 (7) (2010)
Anne Lopes, Marcel Schmidt am Busch, Thomas Simonson
Computational design of protein-ligand binding: Modifying the specificity of asparaginyl-tRNA synthetase. J. Comput. Chem. 31 (6) (2010)
Alexey Aleksandrov, Thomas Simonson
Molecular mechanics models for tetracycline analogs. J. Comput. Chem. 30 (2) (2009)
Guillaume Launay, Thomas Simonson
Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. BMC Bioinform. 9 (2008)
Marcel Schmidt am Busch, Anne Lopes, David Mignon, Thomas Simonson
Computational protein design: Software implementation, parameter optimization, and performance of a simple model. J. Comput. Chem. 29 (7) (2008)
Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Christine Bathelt, Thomas Simonson
Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. BMC Bioinform. 9 (2008)
Guillaume Launay, Raul Mendez, Shoshana J. Wodak, Thomas Simonson
Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets. BMC Bioinform. 8 (2007)
Alexey Aleksandrov, Thomas Simonson
The tetracycline: Mg2+ complex: A molecular mechanics force field. J. Comput. Chem. 27 (13) (2006)
Siegfried Höfinger, Thomas Simonson
Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges. J. Comput. Chem. 22 (3) (2001)
François Wagner, Thomas Simonson
Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect. J. Comput. Chem. 20 (3) (1999)