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2020 – today
- 2020
[j21]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)
2010 – 2019
- 2019
- [j20]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): 127-136 (2019) - 2017
- [j19]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): 2396-2410 (2017) - [j18]Eleni Michael, Savvas Polydorides, Thomas Simonson, Georgios Archontis:
Simple models for nonpolar solvation: Parameterization and testing. J. Comput. Chem. 38(29): 2509-2519 (2017) - 2016
- [j17]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): 404-415 (2016) - [j16]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): 1781-1793 (2016) - 2014
- [j15]Thomas Gaillard, Thomas Simonson:
Pairwise decomposition of an MMGBSA energy function for computational protein design. J. Comput. Chem. 35(18): 1371-1387 (2014) - 2013
- [j14]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): 836-846 (2013) - [j13]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): 2472-2484 (2013) - [j12]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): 2742-2756 (2013) - 2011
- [j11]Guillaume Launay, Thomas Simonson:
A large decoy set of protein-protein complexes produced by flexible docking. J. Comput. Chem. 32(1): 106-120 (2011) - 2010
- [j10]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): 1273-1286 (2010) - [j9]Alexey Aleksandrov, Thomas Simonson:
A molecular mechanics model for imatinib and imatinib: kinase binding. J. Comput. Chem. 31(7): 1550-1560 (2010)
2000 – 2009
- 2009
- [j8]Alexey Aleksandrov, Thomas Simonson:
Molecular mechanics models for tetracycline analogs. J. Comput. Chem. 30(2): 243-255 (2009) - 2008
- [j7]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) - [j6]Guillaume Launay, Thomas Simonson:
Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. BMC Bioinform. 9 (2008) - [j5]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): 1092-1102 (2008) - 2007
- [j4]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) - 2006
- [j3]Alexey Aleksandrov, Thomas Simonson:
The tetracycline: Mg2+ complex: A molecular mechanics force field. J. Comput. Chem. 27(13): 1517-1533 (2006) - 2001
- [j2]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): 290-305 (2001)
1990 – 1999
- 1999
- [j1]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): 322-335 (1999)
Coauthor Index
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