Recent publications

2012

• P. Satpati & T. Simonson (2012) Proteins, in press, 0000.

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

• P. Satpati & T. Simonson (2012) Biochemistry, in press, 0000.

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

• J-P. Colletier, A. Aleksandrov, N. Coquelle, S. Mraihi, E. Mendoza-Barber, M. Field & D. Madern (2012) Molecular Biology and Evolution, in press, 0000, doi: 10.1093/molbev/mss015.

    Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions.

• 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.

      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, 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.

• A. Aleksandrov & M. Field (2011) Physical Chemistry Chemical Physics, 13, 10503-9.

    Efficient solvent boundary potential for hybrid potential simulations.

• N. V. Valeyev & A. Aleksandrov (2011) Theoretical Chemistry Accounts, 129, 747-756.

      An atomistic model for simulations of nilotinib and nilotinib/kinase binding.

2010

• A. Trivella, T. Gaillard, R. H. Stote & P. Hellwig (2010) Journal of Chemical Physics, 132, 115105.

    Far infrared spectra of solid state aliphatic amino acids in different protonation states.

• 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.