Recent publications

2023

• E. Michael, R. Saint-Jalme, D. Mignon & T. Simonson (2023) Frontiers in Molecular Biosciences, 9, 905588. doi.org/10.1016/j.sbi.2021.07.011

      Computational protein design repurposed to explore enzyme vitality and help predict antibiotic resistance

• V. Opuu, G. Nigro, C. Lazennec-Schurdevin, Y. Mechulam, E. Schmitt & T. Simonson (2023) Protein Science, 32, e4738. doi.org/10.1002/pro.4738

      Redesigning methionyl-tRNA synthetase for beta-methionine activity with adaptive landscape flattening and experiments

• X. Chen, N. Ferchaud, P. Briozzo, D. Machover & T. Simonson (2023) Biochemistry, in press, 000. doi.org/10.3389/fmolb.2022.886358

      The PLP-dependent enzyme methionine gamma-lyase: insights into the Michaelis complex from molecular dynamics and free energy simulations

2022

• E. Michael & T. Simonson (2022) Current Opinion in Structural Biology, 72, 46-54. doi.org/10.1016/j.sbi.2021.07.011

      How much can physics do for protein design?

• X. Chen, P. Briozzo, D. Machover & T. Simonson (2022) Frontiers in Molecular Biosciences, 9, 886358. doi.org/10.3389/fmolb.2022.886358

      A computational model for the PLP-dependent enzyme methionine γ-lyase

2021

• T. Simonson, editor (2022) Methods in Molecular Biology, Springer Protocols vol. 2405, Humana Press. doi.org/10.1007/978-1-0716-1855-4

      Computational Peptide Science (book, 424 pages)

• V. Opuu, D. Mignon & T. Simonson (2021) In Methods in Molecular Biology: Computational Peptide Science, editor: T. Simonson. Springer Verlag, New York.

      A knowledge-based unfolded state model for protein design"

2020

• D. Mignon, K. Druart, E. Michael, V. Opuu, S. Polydorides, F. Villa, T. Gaillard, N. Panel, G. Archontis & T. Simonson (2020) Journal of Physical Chemistry A, 124, 10637-10648. doi.org/10.1021/acs.jpca.0c07605

      Physics-based computational protein design: an update. (Feature Article)

• V. Opuu, Y.J. Sun, Titus Hou, Nicolas Panel, Ernesto J. Fuentes & T. Simonson (2020) Scientific Reports, 10, 11150. doi.org/10.1038/s41598-020-67972-w

      A physics-based energy function allows the computational design of a PDZ domain.

• A. H. Mazarek, L. Szeleszczuk, T. Simonson & D. M. Pisklak (2020) International Journal of Molecular Sciences, 21, 6411. doi.org/10.3390/ijms21176411

      Application of various molecular modelling methods in the study of estrogens and xenoestrogens.

• E. Michael, S. Polydorides, T. Simonson & G. Archontis (2020) Journal of Chemical Physics, 153, 054113. doi.org/10.1063/5.0013320

      Hybrid MC/MD for protein design. (Invited article; special issue on molecular dynamics)

• V. Opuu, G. Nigro, T. Gaillard, Y. Mechulam, E. Schmitt & T. Simonson (2020) PLoS Computational Biology, 16, e1007600. doi.org/10.1371/journal.pcbi.1007600

      Adaptive landscape flattening allows the design of both enzyme-substrate binding and catalytic power.

• N. Panel, V. Opuu, F. Villa, D. Mignon & T. Simonson (2020) In "Methods in Molecular Biology: PDZ domains" editor: JP Borg. Springer Verlag, New York.

      Computational design of PDZ:peptide binding.

2019

• Thomas Simonson (2019) The Proteus software for computational protein design (220 pages). Ecole Polytechnique, Paris. https://proteus.polytechnique.fr

• A. Charpentier, D. Mignon, S. Barbe, J. Cortes, T. Schiex, T. Simonson & D. Allouche (2019) Journal of Chemical Information and Modelling, 59, 127-36. doi.org/10.1021/acs.jcim.8b00510

      Variable Neighborhood Search with Cost Function Networks to solve large computational protein design problems.

2018

• V. Opuu, M. Silvert & T. Simonson (2018) Scientific Reports, 7, 15873. doi.org/10.1038/s41598-017-16221-8>

      Computational design of fully overlapping coding schemes for protein pairs and triplets.

• F. Villa & T. Simonson (2018) Journal of Chemical Theory and Computation, 14, 6714-21. doi.org/10.1021/acs.jctc.8b00970

      Protein pKas from adaptive landscape flattening instead of constant-pH simulations.

• F. Villa, N. Panel, X. Chen & T. Simonson (2018) Journal of Chemical Physics, 149, 072302. doi.org/10.1063/1.5022249

      Adaptive landscape flattening in amino acid sequence space for the computational design of protein:peptide binding. (Invited article; special issue on sampling; cover article)

• F. Villa, A. MacKerell Jr., B. Roux & T. Simonson (2018) Journal of Physical Chemistry A, 122, 6147-55. doi.org/10.1021/acs.jpca.8b04418

      Classical Drude polarizable force field model for methyl phosphate and its interactions with Mg. (Selected for a virtual special issue on new methods)

• N. Panel, F. Villa, E. J. Fuentes & T. Simonson (2018) Biophysical Journal, 114, 1091-1102. doi.org/10.1016/j.bpj.2018.01.008

      Accurate PDZ:peptide binding specificity with additive and polarizable free energy simulations.

2017

• N. Panel, Y.J. Sun, E. Fuentes & T. Simonson (2017) Frontiers in Molecular Biosciences, 4, art. 65. doi.org/10.3389/fmolb.2017.00065

      A simple PB/LIE free energy function accurately predicts the peptide binding specificity of the Tiam1 PDZ domain. (Invited article)

• T. Gaillard & T. Simonson (2017) Journal of Chemical Theory and Computation, 13, 4932-43. doi.org/10.1021/acs.jctc.7b00202

      Full protein sequence redesign with an MMGBSA energy function.

• F. Villa, D. Mignon, S. Polydorides & T. Simonson (2017) Journal of Computational Chemistry, 38, 2396-2410. doi.org/10.1002/jcc.24898

      Comparing pairwise-additive and many-body Generalized Born models for acid/base calculations and protein design.

• S. Polydorides, E. Michael, T. Simonson & G. Archontis (2017) Journal of Computational Chemistry, 38, 2509-19. doi.org/10.1002/jcc.24910

      Simple models for nonpolar solvation: parameterization and testing.

• Thomas Simonson, Gerhard Hummer & Benoit Roux (2017) Journal of Physical Chemistry A, 121, 1525-30. doi.org/10.1021/acs.jpca.6b1269

      Equivalence of M- and P-summation in calculations of ionic solvation free energies.

• D. Mignon, N. Panel, X. Chen, E. Fuentes & T. Simonson (2017) Journal of Chemical Theory and Computation, 13, 2271-89. doi.org10.1021/acs.jctc.6b01255

      Computational design of the Tiam1 PDZ domain and its ligand binding.

• K. Druart, M. Le Guennec, Z. Palmai & T. Simonson (2017) Journal of Molecular Graphics and Modelling, 71, 192-99. doi.org/10.1016/j.jmgm.2016.11.007

      Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics.

2016

• K. Druart, J. Bigot, E. Audit & T. Simonson (2016) Journal of Chemical Theory and Computation, 12, 6035-48. doi.org/10.1021/acs.jctc.6b00421

      A hybrid Monte Carlo scheme for multibackbone protein design.

• D. Mignon & T. Simonson (2016) Journal of Computational Chemistry, 37, 1781-93. doi.org/10.1002/jcc.24393

      Comparing three stochastic search algorithms for computational protein design: Monte Carlo, Replica Exchange Monte Carlo, and a multistart, steepest-descent heuristic.

• S. Polydorides, E. Michael, D. Mignon, K. Druart, G. Archontis & T. Simonson (2016) In "Methods in Molecular Biology: Design and Creation of Protein Ligand Binding Proteins," editor: Barry Stoddard. Springer Verlag, New York.

      Proteus and the design of ligand binding sites.

• T. Simonson & B. Roux (2016) Molecular Simulation, 42, 1090-1101. doi.org/10.1080/08927022.2015.1121544

      Concepts and protocols for electrostatic free energies. (Invited article, recommended by Faculty 1000)

• T. Gaillard, N. Panel & T. Simonson (2016) Proteins, 84, 803-819. doi.org/10.1002/prot.25030

      Protein sidechain conformation predictions with an MMGBSA energy function.

• T. Simonson, S. Ye-Lehmann, Z. Palmai, N. Amara, S. Wydau-Dematteis, E. Bigan, K. Druart, C. Moch & P. Plateau (2016) Proteins, 84, 240-253. doi.org/10.1002/prot.24972

      Redesigning the sterospecificity of tyrosyl-tRNA synthetase. (Cover article)

• K. Druart, Z. Palmai, E. Omarjee & T. Simonson (2016) Journal of Computational Chemistry, 37, 404-15. doi.org/10.1002/jcc.24230

      Protein:ligand binding free energies: a stringent test for computational protein design.

2015

• T. Simonson (2015) In "In silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications" , editor: Claudio Cavasotto. CRC Press, New York.

      Chapter one: the physical basis of ligand binding.

• T. Simonson, A. Aleksandrov & P. Satpati (2015) Biochemical and Biophysical Archives General Subjects, 1850. 1006-16. doi.org/10.1016/j.bbagen.2014.07.006

      Electrostatic free energies in GTPases: classic allostery and the rest. (Invited article)

• M. Kumar, T. Simonson, G. Ohanessian & C. Clavaguera (2015) ChemPhysChem, 16, 658-65. doi.org/10.1002/cphc.201402685

      Structure and thermodynamics of Mg:phosphate interactions in water: a simulation study.

2014

• Y.-L. Lin, A. Aleksandrov, T. Simonson & B. Roux (2014) Journal of Chemical Theory and Computation, 10, 2690-2709. doi.org/10.1021/ct500195p

      An overview of electrostatic free energy computations for solutions and proteins. (Invited article)

• T. Gaillard & T. Simonson (2014) Journal of Computational Chemistry, 35, 1371-1387. doi.org/10.1002/jcc.23637

      Pairwise Decomposition of an MMGBSA Energy Function for Computational Protein Design.

2013

• T. Simonson, T. Gaillard, D. Mignon, M. Schmidt am Busch, A. Lopes, N. Amara, S. Polydorides, A. Sedano, K. Druart & G. Archontis (2013) Journal of Computational Chemistry, 34, 2472-84.

      Computational protein design: the Proteus software and selected applications.

• T. Simonson (2013) Journal of Chemical Theory and Computation, 9, 4603–4608.

      What is the dielectric constant of a protein when its backbone is fixed?

• S. Polydorides & T. Simonson (2013) Journal of Computational Chemistry, 34, 2742–56.

      Monte Carlo simulations of proteins at constant pH with generalized Born solvent.

• T. Simonson (2013) Current Pharmaceutical Design, 19, 4241-56.

      Protein:ligand recognition: simple models for electrostatic effects.

• T. Simonson & P. Satpati (2013) Journal of Computational Chemistry, 34, 836-46.

      Simulating GTP:Mg and GDP:Mg with a simple force field: a structural and thermodynamic analysis.

• T. Gaillard, B.B.L. Schwarz, Y. Chebaro, R.H. Stote & A. Dejaegere (2013) Journal of Chemical Information and Modeling, 53, 2471-2482.

      Protein Structural Statistics with PSS.

2012

• T. Simonson & P. Satpati (2012) Proteins, 80, 2742-57.

      Nucleotide recognition by the initiation factor aIF5B: free energy simulations of a neo-classical GTPase.

• P. Satpati & T. Simonson (2012) Proteins, 80, 1264–82.

      Conformational selection through electrostatics: free energy simulations of GTP and GDP binding to archaeal Initiation Factor 2.

• P. Satpati & T. Simonson (2012) Biochemistry, 51, 353–61.

      Conformational selection by the aIF2 GTPase: a molecular dynamics study of functional pathways.

• M. Schmidt am Busch, A. Lopes, D. Mignon, T. Gaillard & T. Simonson (2012) In Quantum Simulations of Materials and Biological Systems (editors: J. Zeng, R. Zhang, H. Treutlein), Springer Verlag, New York. Pages 121-140.

      The inverse protein folding problem: protein design and structure prediction in the genomic era.

2011

• T. Gaillard & D. A. Case (2011) Journal of Chemical Theory and Computation, 7, 3181-3198.

      Evaluation of DNA Force Fields in Implicit Solvation.

• S. Polydorides, N. Amara, C. Aubard, P. Plateau, T. Simonson & G. Archontis (2011) Proteins, 79, 3448-3468.

      Computational protein design with a generalized Born solvent model: application to asparaginyl-tRNA synthetase.

• P. Satpati, C. Clavaguera, G. Ohanessian & T. Simonson (2011) Journal of Physical Chemistry B, 115, 6749-63.

      Free energy simulations of a GTPase: GTP and GDP binding to archaeal Initiation Factor 2.

• G. Launay & T. Simonson (2011) Journal of Computational Chemistry, 32, 106-120.

      A large decoy set of protein-protein complexes produced by flexible docking.

2010

• A. Aleksandrov, S. Polydorides, G. Archontis & T. Simonson (2010) Journal of Physical Chemistry B, 114, 10634-10648.

      Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized Born solvent.

• M. Schmidt am Busch, A. Sedano & T. Simonson (2010) Plos One, 5(5), e10410.

      Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition.

• A. Aleksandrov & T. Simonson (2010) Journal of Biological Chemistry, 285, 13807-13815.

      Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases.

• D. Dalm, G. Palm, A. Aleksandrov, T. Simonson & W. Hinrichs (2010) Journal of Molecular Biology, 398, 83-96.

      Non-antibiotic properties of tetracyclines: structural basis for inhibition of secretory Phospholipase A2.

• A. Aleksandrov, D. Thompson & T. Simonson (2010) Journal of Molecular Recognition, 23, 117-127.

      Alchemical free energy simulations for biological complexes: powerful but temperamental....

• A. Aleksandrov & T. Simonson (2010) Journal of Computational Chemistry, 31, 1550-1560.

      A molecular mechanics model for imatinib and imatinib:kinase binding.

• A. Lopes, M. Schmidt am Busch & T. Simonson (2010) Journal of Computational Chemistry, 31, 1273-1286.

      Computational design of protein:ligand binding: modifying the specificity of asparaginyl-tRNA synthetase.

2009

• M. Schmidt am Busch, D. Mignon & T. Simonson (2009) Proteins, 77, 139–158.

      Computational protein design as a tool for fold recognition.

• A. Aleksandrov, L. Schuldt, W. Hinrichs & T. Simonson (2009) Biophysical Journal, 97, 2829–2838.

      Tetracycline-Tet Repressor binding specificity: insights from experiments and simulations.

• A. Aleksandrov & T. Simonson (2009) Journal of Computational Chemistry, 30, 243-255.

      Molecular mechanics models for tetracycline analogs.

2008

• A. Aleksandrov & T. Simonson (2008) Biochemistry, 47,13594–13603.

      Binding of tetracyclines to elongation factor Tu, the Tet Repressor, and the ribosome: a molecular dynamics simulation study.

• A. Aleksandrov, L. Schuldt, W. Hinrichs & T. Simonson (2008) Journal of Molecular Biology, 378, 896-910.

      Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallographic study.

• A. Aleksandrov & T. Simonson (2008) Journal of the American Chemical Society, 130, 1114-1115.

      Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site.

• J. Noirel & T. Simonson (2008) Journal of Chemical Physics, 129, 185104-185112.

      Neutral evolution of proteins:  the superfunnel in sequence space and its relation to mutational robustness.

• G. Launay & T. Simonson (2008) BMC Bioinformatics, 9, 427-443.

      Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations.

• M. Schmidt am Busch, A. Lopes, N. Amara, C. Bathelt & T. Simonson (2008) BMC Bioinformatics, 9, 148-163.

     Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.

• M. Schmidt am Busch, A. Lopes, D. Mignon & T. Simonson (2008) Journal of Computational Chemistry, 29, 1092-1102.

      Computational protein design: software implementation, parameter optimization, and performance of a simple method.

• T. Simonson (2008) Photosynthesis Research, 97, 21-32.

      Dielectric relaxation in proteins: the computational perspective.

• D. Thompson, C. Lazennec, P. Plateau & T. Simonson (2008) Proteins, 71, 1450-1460.

      Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations.

2007

• D. Thompson, C. Lazennec, P. Plateau & T. Simonson (2007) Journal of Biological Chemistry, 282, 30856-30868.

      Ammonium scanning in an enzyme active site: the chiral specificity of aspartyl-tRNA synthetase.

• J. Noirel & T. Simonson (2007) BMC Structural Biology, 7, 79-93.

      Neutral evolution of protein-protein interactions: a computational study using simple models.

• G. Launay, R. Mendez, S. Wodak, T. Simonson (2007) BMC Bioinformatics, 8, 270-278.

      Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.

• A. Lopes, A. Alexandrov, C. Bathelt, G. Archontis & T. Simonson (2007) Proteins, 67, 853-867.

      Computational sidechain placement and protein mutagenesis with implicit solvent models.

• A. Alexandrov, J. Proft, W. Hinrichs & T. Simonson (2007) ChemBioChem, 8, 675- 685.

      Protonation patterns in tetracycline:Tet Repressor recognition: simulations and experiments.

2006

• A. Alexandrov & T. Simonson (2006) Journal of Computational Chemistry, 27, 1517-1533.

      The tetracycline:Mg2+ complex: a molecular mechanics force field.

• D. Thompson & T. Simonson (2006) Journal of Biological Chemistry, 281, 23792-23803.

      Molecular dynamics simulations show that bound Mg2+  contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions.

• D. Thompson, P. Plateau & T. Simonson (2006) ChemBioChem, 7, 337-344.

      Free energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase.

• T. Simonson (2006) in Free energy calculations: theory and applications in chemistry and biology (Editors: C. Chipot & A. Pohorille; Springer Verlag, New York).
      Free energy calculations: approximate methods for biological macromolecules.

• C. Chipot, A.E. Mark, V.S. Pande & T. Simonson (2006) in Free energy calculations: theory and applications in chemistry and biology (Editors: C. Chipot & A. Pohorille; Springer Verlag, New York).
      Significant applications of free energy calculations to chemistry and biology.

2005

• G. Archontis & T. Simonson (2005) Journal of Physical Chemistry B, 109, 22667-22673.
      A residue-pairwise Generalized Born model suitable for protein design calculations.

• N. Calimet & T. Simonson (2005) Journal of Molecular Graphics and Modelling, 24, 404-411.
      Cys_xHis_y-Zn²⁺ interactions: possibilities and limitations of a simple pairwise force field.

• T. Simonson (2005) Médecine et Sciences, 21, 609-612.
      Le problème du repliement: peut-on prédire la structure des protéines?

• G. Archontis & T. Simonson (2005) Biophysical Journal,  88, 3888-3904.
      Proton binding to proteins: a free energy component analysis using a dielectric continuum model.

2004 and earlier

• J. Janin & T. Simonson, Invited Editors (2004) Current Opinion in Structural Biology, 14, 189-191.
     Theory and Simulation Section:  from protons to genomes.

• T. Simonson, J. Carlsson & D. Case (2004) Journal of the American Chemical Society, 126, 4167-4180.
  Proton binding to proteins: pKa calculations with explicit and implicit solvent models.

• L. Moulinier, D. Case & T. Simonson (2003) Acta Crystallographica D, 59, 2094-2103.
  Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum.

• T. Simonson (2003) Reports on Progress in Physics, 66, 737-787.
    Electrostatics and dynamics of proteins.

• T. Simonson (2002) Proc. Nat. Acad. Sci. (USA), 99, 6544-6549. Gaussian fluctuations and linear response in an electron transfer protein.

• T. Simonson & N. Calimet (2002) Proteins, 49, 37-48.
  Cys_xHis_y-Zn²⁺ interactions: thiol vs. thiolate coordination.

• T. Simonson, G. Archontis & M. Karplus (2002) Accts. Chem. Res., 35, 430-437. Protein-ligand recognition: free energy simulations come of age.

• M. Nina & T. Simonson (2002) J. Phys. Chem. B, 106, 3696-3705. Molecular dynamics of the tRNA(Ala) acceptor stem: comparison between continuum reaction field and particle-mesh Ewald electrostatic treatments.

• G. Archontis & T. Simonson (2001) J. Am. Chem. Soc., 123, 11047-11056. A Poisson-Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation.

• N. Calimet, M. Schaefer & T. Simonson (2001) Proteins , 45, 144-158. Protein molecular dynamics with the Generalized Born/ACE solvent model.

• A.T.Brunger, P.D.Adams, W.L.DeLano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, N.S.Pannu, R.J.Read, L.M.Rice & T.Simonson (2001) International Tables of Crystallography, Volume F,
  Editors: M.G. Rossmann and E. Arnold; Dordrecht: Kluwer Academic Publishers, the Netherlands.
  The structure determination language of the Crystallography and NMR System.

• T. Simonson (2001) Current Opinion in Structural Biology , 11, 243-252. Macromolecular electrostatics: continuum models and their growing pains.

• G. Archontis, T. Simonson & M. Karplus (2001) Journal of Molecular Biology, 306, 307-327. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.

• S. Hoefinger & T. Simonson (2001) Journal of Computational Chemistry, 22, 290-305. Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges.

• T. Simonson (2000) Computational Biochemistry and Biophysics (Eds. O. Becker, A. MacKerell, B. Roux, M. Watanabe; Marcel Dekker, New York), Chapter 5, 169-197. Free energy calculations.

• T. Simonson (2000) Journal of Physical Chemistry B, 104, 6509-6513. Electrostatic free energy calculations for macromolecules: a hybrid molecular dynamics/continuum electrostatics approach.

• T. Simonson, G. Archontis & M. Karplus (1999) J. Phys. Chem. B, 103, 6142-6156. A Poisson-Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation.

• T. Simonson (1999) International Journal of Quantum Chemistry, 73, 45-57. Dielectric relaxation in proteins: microscopic and macroscopic models.

• B. Roux & T. Simonson (1999) Biophysical Chemistry, 78, 1-20. Implicit solvent models.

• J. Zeng, H. Treutlein & T. Simonson (1999) Proteins, 35, 89-100. Molecular dynamics simulations of the Ras:Raf and Rap:Raf complexes.

• J. Zeng, M. Fridman, H. Maruta, H. Treutlein & T. Simonson (1999) Protein Science, 8, 50-64. Protein--protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding.

• F. Wagner & T. Simonson (1999) J. Comp. Chem., 20, 322-335. Implicit solvent models: combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect.

• T. Simonson (1998) J. Am. Chem. Soc., 120, 4875-4876. The dielectric constant of cytochrome c from molecular dynamics simulations in a water droplet with no electrostatic cutoff.

• J. Arnez, K. Flanagan, D. Moras & T. Simonson (1998) Proteins, 32, 362-380. Engineering a Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiment.

• A.T.Brunger, P.D.Adams, G.M.Clore,W.L.DeLano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, & G.L.Warren (1998) Acta Cryst. D54, 905-921.
  Crystallography and NMR System (CNS): a new software system for macromolecular structure determination.

• J. Zeng, H. Treutlein & T. Simonson (1998) Proteins, 31, 186-200. Conformation of the Ras recognition helix of Raf studied by molecular dynamics and free energy simulations.

• G. Archontis, T. Simonson, D. Moras & M. Karplus (1998) J. Molec. Biol., 275, 823-846. Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations.

• T. Simonson, G. Archontis & M. Karplus (1997) J. Phys. Chem. B, 101, 8349-8362. Continuum treatment of long-range interactions in macromolecular free energy calculations. Application to protein-ligand binding.

• T. Simonson, C. Wong & A.T. Brunger (1997) J. Phys. Chem. A, 101, 1935-1945. Classical and quantum simulations of tryptophan in water.

• T. Simonson (1997) Pacific Symposium on Biocomputing (Ed. R. Altman, World Scientific, Singapore). Novel linear response and hybrid continuum-molecular dynamics methodologies.

• T. Simonson (1997) Ordinateurs et calcul parallele (Ed. M. Cosnard, OFTA, Paris). Calcul parallele et intensif en biologie moleculaire et en chimie.

• T. Simonson & C.L. Brooks (1996) J. Am. Chem. Soc., 118, 8452-8458. Charge screening and the dielectric constant of proteins: insights from molecular dynamics.

• T. Simonson (1996) Chem. Phys. Lett., 250, 450-454. Accurate calculation of the dielectric constant of water from simulations of a microscopic droplet in vacuum.

• T. Simonson & D. Perahia (1996) Far. Disc. Chem. Soc., 103, 71-90. Polar fluctuations in proteins: molecular dynamics studies of cytochrome c in aqueous solution.

• T. Simonson & D. Perahia (1995) Proc. Nat. Acad. Sci. (U.S.A.), 92, 1082-1086. Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution.

• T. Simonson & D. Perahia (1995) J. Am. Chem. Soc., 117, 7987-8000. Microscopic dielectric properties of cytochrome c from molecular dynamics simulations.

• T. Simonson & D. Perahia (1995) Comp. Phys. Comm., 91, 291-303. Dielectric properties of proteins from computer simulations: tools and techniques.

• Hodel, A., Rice, L., Simonson, T., Fox, R. & Brunger, A.T. (1995) Protein Science, 4, 636-654. Proline cis-trans isomerization in Staphylococcal nuclease: multi-substate free energy perturbation calculations.