| Year |
Citation |
Score |
| 2023 |
Chen X, Ferchaud N, Briozzo P, Machover D, Simonson T. PLP-Dependent Enzyme Methionine γ-Lyase: Insights into the Michaelis Complex from Molecular Dynamics and Free Energy Simulations. Biochemistry. PMID 37668546 DOI: 10.1021/acs.biochem.3c00355 |
0.378 |
|
| 2022 |
Chen X, Briozzo P, Machover D, Simonson T. A Computational Model for the PLP-Dependent Enzyme Methionine -Lyase. Frontiers in Molecular Biosciences. 9: 886358. PMID 35558556 DOI: 10.3389/fmolb.2022.886358 |
0.395 |
|
| 2022 |
Opuu V, Mignon D, Simonson T. Knowledge-Based Unfolded State Model for Protein Design. Methods in Molecular Biology (Clifton, N.J.). 2405: 403-424. PMID 35298824 DOI: 10.1007/978-1-0716-1855-4_19 |
0.319 |
|
| 2021 |
Michael E, Simonson T. How much can physics do for protein design? Current Opinion in Structural Biology. 72: 46-54. PMID 34461593 DOI: 10.1016/j.sbi.2021.07.011 |
0.371 |
|
| 2021 |
Panel N, Villa F, Opuu V, Mignon D, Simonson T. Computational Design of PDZ-Peptide Binding. Methods in Molecular Biology (Clifton, N.J.). 2256: 237-255. PMID 34014526 DOI: 10.1007/978-1-0716-1166-1_14 |
0.351 |
|
| 2020 |
Mignon D, Druart K, Michael E, Opuu V, Polydorides S, Villa F, Gaillard T, Panel N, Archontis G, Simonson T. Physics-Based Computational Protein Design: An Update. The Journal of Physical Chemistry. A. PMID 33170681 DOI: 10.1021/acs.jpca.0c07605 |
0.331 |
|
| 2020 |
Mazurek AH, Szeleszczuk Ł, Simonson T, Pisklak DM. Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens. International Journal of Molecular Sciences. 21. PMID 32899216 DOI: 10.3390/Ijms21176411 |
0.342 |
|
| 2020 |
Michael E, Polydorides S, Simonson T, Archontis G. Hybrid MC/MD for protein design. The Journal of Chemical Physics. 153: 054113. PMID 32770896 DOI: 10.1063/5.0013320 |
0.427 |
|
| 2020 |
Opuu V, Sun YJ, Hou T, Panel N, Fuentes EJ, Simonson T. A physics-based energy function allows the computational redesign of a PDZ domain. Scientific Reports. 10: 11150. PMID 32636412 DOI: 10.1038/S41598-020-67972-W |
0.481 |
|
| 2020 |
Opuu V, Nigro G, Gaillard T, Schmitt E, Mechulam Y, Simonson T. Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power. Plos Computational Biology. 16: e1007600. PMID 31917825 DOI: 10.1371/Journal.Pcbi.1007600 |
0.421 |
|
| 2019 |
Villa F, MacKerell AD, Roux B, Simonson T. Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg". The Journal of Physical Chemistry. A. PMID 30600990 DOI: 10.1021/Acs.Jpca.8B12337 |
0.305 |
|
| 2018 |
Villa F, Simonson T. Protein pKa's from adaptive landscape flattening instead of constant-pH simulations. Journal of Chemical Theory and Computation. PMID 30431264 DOI: 10.1021/Acs.Jctc.8B00970 |
0.409 |
|
| 2018 |
Charpentier A, Mignon D, Barbe S, Cortes J, Schiex T, Simonson T, Allouche D. Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems. Journal of Chemical Information and Modeling. PMID 30380857 DOI: 10.1021/Acs.Jcim.8B00510 |
0.353 |
|
| 2018 |
Villa F, Panel N, Chen X, Simonson T. Adaptive landscape flattening in amino acid sequence space for the computational design of protein:peptide binding. The Journal of Chemical Physics. 149: 072302. PMID 30134674 DOI: 10.1063/1.5022249 |
0.419 |
|
| 2018 |
Villa F, MacKerell AD, Roux B, Simonson T. Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg. The Journal of Physical Chemistry. A. PMID 29966419 DOI: 10.1021/Acs.Jpca.8B04418 |
0.49 |
|
| 2018 |
Kumar M, Simonson T, Ohanessian G, Clavaguéra C. Corrigendum: Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 19: 1117. PMID 29733114 DOI: 10.1002/Cphc.201800205 |
0.344 |
|
| 2018 |
Panel N, Villa F, Fuentes EJ, Simonson T. Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations. Biophysical Journal. 114: 1091-1102. PMID 29539396 DOI: 10.1016/J.Bpj.2018.01.008 |
0.487 |
|
| 2017 |
Panel N, Sun YJ, Fuentes EJ, Simonson T. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain. Frontiers in Molecular Biosciences. 4: 65. PMID 29018806 DOI: 10.3389/Fmolb.2017.00065 |
0.484 |
|
| 2017 |
Gaillard T, Simonson T. Full Protein Sequence Redesign with an MMGBSA Energy Function. Journal of Chemical Theory and Computation. 13: 4932-4943. PMID 28886244 DOI: 10.1021/Acs.Jctc.7B00202 |
0.444 |
|
| 2017 |
Michael E, Polydorides S, Simonson T, Archontis G. Simple models for nonpolar solvation: Parameterization and testing. Journal of Computational Chemistry. 38: 2509-2519. PMID 28786118 DOI: 10.1002/Jcc.24910 |
0.476 |
|
| 2017 |
Villa F, Mignon D, Polydorides S, Simonson T. Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design. Journal of Computational Chemistry. 38: 2396-2410. PMID 28749575 DOI: 10.1002/Jcc.24898 |
0.426 |
|
| 2017 |
Mignon D, Panel N, Chen X, Fuentes EJ, Simonson T. Computational design of the Tiam1 PDZ domain and its ligand binding. Journal of Chemical Theory and Computation. PMID 28394603 DOI: 10.1021/Acs.Jctc.6B01255 |
0.433 |
|
| 2017 |
Simonson T, Hummer G, Roux B. On the Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies. The Journal of Physical Chemistry. A. PMID 28152306 DOI: 10.1021/Acs.Jpca.6B12691 |
0.367 |
|
| 2016 |
Druart K, Guennec ML, Palmai Z, Simonson T. Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics. Journal of Molecular Graphics & Modelling. 71: 192-199. PMID 27939931 DOI: 10.1016/J.Jmgm.2016.11.007 |
0.407 |
|
| 2016 |
Druart K, Bigot J, Audit E, Simonson T. A hybrid Monte Carlo scheme for multibackbone protein design. Journal of Chemical Theory and Computation. PMID 27775883 DOI: 10.1021/Acs.Jctc.6B00421 |
0.44 |
|
| 2016 |
Mignon D, Simonson T. Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic. Journal of Computational Chemistry. 37: 1781-93. PMID 27197555 DOI: 10.1002/Jcc.24393 |
0.424 |
|
| 2016 |
Polydorides S, Michael E, Mignon D, Druart K, Archontis G, Simonson T. Proteus and the Design of Ligand Binding Sites. Methods in Molecular Biology (Clifton, N.J.). 1414: 77-97. PMID 27094287 DOI: 10.1007/978-1-4939-3569-7_6 |
0.461 |
|
| 2016 |
Gaillard T, Panel N, Simonson T. Protein side chain conformation predictions with an MMGBSA energy function. Proteins. 84: 803-19. PMID 26948696 DOI: 10.1002/Prot.25030 |
0.398 |
|
| 2016 |
Simonson T, Ye-Lehmann S, Palmai Z, Amara N, Wydau-Dematteis S, Bigan E, Druart K, Moch C, Plateau P. Redesigning the stereospecificity of tyrosyl-tRNA synthetase. Proteins. 84: 240-53. PMID 26676967 DOI: 10.1002/Prot.24972 |
0.429 |
|
| 2016 |
Druart K, Palmai Z, Omarjee E, Simonson T. Protein:Ligand binding free energies: A stringent test for computational protein design. Journal of Computational Chemistry. 37: 404-15. PMID 26503829 DOI: 10.1002/Jcc.24230 |
0.501 |
|
| 2016 |
Simonson T, Roux B. Concepts and protocols for electrostatic free energies Molecular Simulation. 42: 1090-1101. DOI: 10.1080/08927022.2015.1121544 |
0.457 |
|
| 2016 |
Litman JM, Joo Sun Y, Hou T, LuCore SD, Panel N, Simonson T, Fuentes EJ, Schnieders MJ. Protein Sequence Optimization with a Polarizable Force Field: Insights from PDZ Domains Biophysical Journal. 110: 345a-346a. DOI: 10.1016/J.Bpj.2015.11.1859 |
0.389 |
|
| 2015 |
Kumar M, Simonson T, Ohanessian G, Clavaguéra C. Structure and thermodynamics of Mg:phosphate interactions in water: a simulation study. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 16: 658-65. PMID 25528981 DOI: 10.1002/Cphc.201402685 |
0.406 |
|
| 2015 |
Simonson T, Aleksandrov A, Satpati P. Electrostatic free energies in translational GTPases: Classic allostery and the rest. Biochimica Et Biophysica Acta. 1850: 1006-16. PMID 25047891 DOI: 10.1016/J.Bbagen.2014.07.006 |
0.758 |
|
| 2014 |
Lin YL, Aleksandrov A, Simonson T, Roux B. An Overview of Electrostatic Free Energy Computations for Solutions and Proteins. Journal of Chemical Theory and Computation. 10: 2690-709. PMID 26586504 DOI: 10.1021/Ct500195P |
0.435 |
|
| 2014 |
Gaillard T, Simonson T. Pairwise decomposition of an MMGBSA energy function for computational protein design. Journal of Computational Chemistry. 35: 1371-87. PMID 24854675 DOI: 10.1002/Jcc.23637 |
0.443 |
|
| 2014 |
Lin YL, Aleksandrov A, Simonson T, Roux B. An overview of electrostatic free energy computations for solutions and proteins Journal of Chemical Theory and Computation. 10: 2690-2709. DOI: 10.1021/ct500195p |
0.306 |
|
| 2013 |
Simonson T. What Is the Dielectric Constant of a Protein When Its Backbone Is Fixed? Journal of Chemical Theory and Computation. 9: 4603-8. PMID 26589172 DOI: 10.1021/Ct400398E |
0.435 |
|
| 2013 |
Polydorides S, Simonson T. Monte Carlo simulations of proteins at constant pH with generalized Born solvent, flexible sidechains, and an effective dielectric boundary. Journal of Computational Chemistry. 34: 2742-56. PMID 24122878 DOI: 10.1002/Jcc.23450 |
0.464 |
|
| 2013 |
Simonson T, Gaillard T, Mignon D, Schmidt am Busch M, Lopes A, Amara N, Polydorides S, Sedano A, Druart K, Archontis G. Computational protein design: the Proteus software and selected applications. Journal of Computational Chemistry. 34: 2472-84. PMID 24037756 DOI: 10.1002/Jcc.23418 |
0.486 |
|
| 2013 |
Simonson T, Satpati P. Simulating GTP:Mg and GDP:Mg with a simple force field: a structural and thermodynamic analysis. Journal of Computational Chemistry. 34: 836-46. PMID 23280996 DOI: 10.1002/Jcc.23207 |
0.715 |
|
| 2013 |
Simonson T. Protein: ligand recognition: simple models for electrostatic effects. Current Pharmaceutical Design. 19: 4241-56. PMID 23170890 DOI: 10.2174/1381612811319230008 |
0.461 |
|
| 2012 |
Simonson T, Satpati P. Nucleotide recognition by the initiation factor aIF5B: free energy simulations of a neoclassical GTPase. Proteins. 80: 2742-57. PMID 22887821 DOI: 10.1002/Prot.24158 |
0.705 |
|
| 2012 |
Satpati P, Simonson T. Conformational selection through electrostatics: Free energy simulations of GTP and GDP binding to archaeal initiation factor 2. Proteins. 80: 1264-82. PMID 22275120 DOI: 10.1002/Prot.24023 |
0.749 |
|
| 2012 |
Satpati P, Simonson T. Conformational selection by the aIF2 GTPase: a molecular dynamics study of functional pathways. Biochemistry. 51: 353-61. PMID 22165972 DOI: 10.1021/Bi201675N |
0.698 |
|
| 2011 |
Polydorides S, Amara N, Aubard C, Plateau P, Simonson T, Archontis G. Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase. Proteins. 79: 3448-68. PMID 21563215 DOI: 10.1002/Prot.23042 |
0.501 |
|
| 2011 |
Satpati P, Clavaguéra C, Ohanessian G, Simonson T. Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2. The Journal of Physical Chemistry. B. 115: 6749-63. PMID 21534562 DOI: 10.1021/Jp201934P |
0.75 |
|
| 2011 |
Launay G, Simonson T. A large decoy set of protein-protein complexes produced by flexible docking. Journal of Computational Chemistry. 32: 106-20. PMID 20623649 DOI: 10.1002/Jcc.21604 |
0.415 |
|
| 2011 |
Satpati P, Clavaguéra C, Ohanessian G, Simonson T. Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2 Journal of Physical Chemistry B. 115: 6749-6763. DOI: 10.1021/jp201934p |
0.709 |
|
| 2010 |
Aleksandrov A, Polydorides S, Archontis G, Simonson T. Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solvent. The Journal of Physical Chemistry. B. 114: 10634-48. PMID 20701391 DOI: 10.1021/Jp104406X |
0.434 |
|
| 2010 |
Schmidt Am Busch M, Sedano A, Simonson T. Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. Plos One. 5: e10410. PMID 20463972 DOI: 10.1371/Journal.Pone.0010410 |
0.341 |
|
| 2010 |
Dalm D, Palm GJ, Aleksandrov A, Simonson T, Hinrichs W. Nonantibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2. Journal of Molecular Biology. 398: 83-96. PMID 20211188 DOI: 10.1016/J.Jmb.2010.02.049 |
0.356 |
|
| 2010 |
Aleksandrov A, Simonson T. Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases. The Journal of Biological Chemistry. 285: 13807-15. PMID 20200154 DOI: 10.1074/Jbc.M110.109660 |
0.439 |
|
| 2010 |
Aleksandrov A, Simonson T. A molecular mechanics model for imatinib and imatinib:kinase binding. Journal of Computational Chemistry. 31: 1550-60. PMID 20020482 DOI: 10.1002/Jcc.21442 |
0.531 |
|
| 2010 |
Lopes A, Schmidt Am Busch M, Simonson T. Computational design of protein-ligand binding: modifying the specificity of asparaginyl-tRNA synthetase. Journal of Computational Chemistry. 31: 1273-86. PMID 19862811 DOI: 10.1002/Jcc.21414 |
0.497 |
|
| 2010 |
Aleksandrov A, Thompson D, Simonson T. Alchemical free energy simulations for biological complexes: powerful but temperamental.... Journal of Molecular Recognition : Jmr. 23: 117-27. PMID 19693787 DOI: 10.1002/Jmr.980 |
0.479 |
|
| 2010 |
Simonson T, Archontis G, Karplus M. ChemInform Abstract: Free Energy Simulations Come of Age: Protein-Ligand Recognition Cheminform. 33: no-no. DOI: 10.1002/chin.200237290 |
0.327 |
|
| 2009 |
Aleksandrov A, Schuldt L, Hinrichs W, Simonson T. Tetracycline-tet repressor binding specificity: insights from experiments and simulations. Biophysical Journal. 97: 2829-38. PMID 19917238 DOI: 10.1016/J.Bpj.2009.08.050 |
0.512 |
|
| 2009 |
am Busch MS, Mignon D, Simonson T. Computational protein design as a tool for fold recognition. Proteins. 77: 139-58. PMID 19408297 DOI: 10.1002/Prot.22426 |
0.399 |
|
| 2009 |
Aleksandrov A, Simonson T. Molecular mechanics models for tetracycline analogs. Journal of Computational Chemistry. 30: 243-55. PMID 18615434 DOI: 10.1002/Jcc.21040 |
0.481 |
|
| 2008 |
Aleksandrov A, Simonson T. Binding of tetracyclines to elongation factor Tu, the Tet repressor, and the ribosome: a molecular dynamics simulation study. Biochemistry. 47: 13594-603. PMID 19032078 DOI: 10.1021/Bi801726Q |
0.472 |
|
| 2008 |
Launay G, Simonson T. Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. Bmc Bioinformatics. 9: 427. PMID 18844985 DOI: 10.1186/1471-2105-9-427 |
0.418 |
|
| 2008 |
Simonson T. Dielectric relaxation in proteins: the computational perspective. Photosynthesis Research. 97: 21-32. PMID 18443919 DOI: 10.1007/S11120-008-9293-2 |
0.435 |
|
| 2008 |
Aleksandrov A, Schuldt L, Hinrichs W, Simonson T. Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallographic study. Journal of Molecular Biology. 378: 898-912. PMID 18395746 DOI: 10.1016/J.Jmb.2008.03.022 |
0.42 |
|
| 2008 |
am Busch MS, Lopes A, Amara N, Bathelt C, Simonson T. Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. Bmc Bioinformatics. 9: 148. PMID 18366628 DOI: 10.1186/1471-2105-9-148 |
0.427 |
|
| 2008 |
Aleksandrov A, Simonson T. Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site. Journal of the American Chemical Society. 130: 1114-5. PMID 18219717 DOI: 10.1021/Ja0741933 |
0.389 |
|
| 2008 |
Thompson D, Lazennec C, Plateau P, Simonson T. Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations. Proteins. 71: 1450-60. PMID 18076053 DOI: 10.1002/Prot.21834 |
0.447 |
|
| 2008 |
Schmidt Am Busch M, Lopes A, Mignon D, Simonson T. Computational protein design: software implementation, parameter optimization, and performance of a simple model. Journal of Computational Chemistry. 29: 1092-102. PMID 18069664 DOI: 10.1002/Jcc.20870 |
0.435 |
|
| 2008 |
Zeng J, Fridman M, Maruta H, Treutlein HR, Simonson T. Protein–protein recognition: An experimental and computational study of the R89K mutation in Raf and its effect on Ras binding Protein Science. 8: 50-64. PMID 10210183 DOI: 10.1110/Ps.8.1.50 |
0.478 |
|
| 2007 |
Noirel J, Simonson T. Neutral evolution of protein-protein interactions: a computational study using simple models. Bmc Structural Biology. 7: 79. PMID 18021454 DOI: 10.1186/1472-6807-7-79 |
0.361 |
|
| 2007 |
Thompson D, Lazennec C, Plateau P, Simonson T. Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase. The Journal of Biological Chemistry. 282: 30856-68. PMID 17690095 DOI: 10.1074/Jbc.M704788200 |
0.438 |
|
| 2007 |
Launay G, Mendez R, Wodak S, Simonson T. Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets. Bmc Bioinformatics. 8: 270. PMID 17662112 DOI: 10.1186/1471-2105-8-270 |
0.408 |
|
| 2007 |
Aleksandrov A, Proft J, Hinrichs W, Simonson T. Protonation patterns in tetracycline:tet repressor recognition: simulations and experiments. Chembiochem : a European Journal of Chemical Biology. 8: 675-85. PMID 17361981 DOI: 10.1002/Cbic.200600535 |
0.496 |
|
| 2007 |
Lopes A, Alexandrov A, Bathelt C, Archontis G, Simonson T. Computational sidechain placement and protein mutagenesis with implicit solvent models. Proteins. 67: 853-67. PMID 17348031 DOI: 10.1002/Prot.21379 |
0.391 |
|
| 2007 |
Roux B, Simonson T. Implicit solvent models. Biophysical Chemistry. 78: 1-20. PMID 17030302 DOI: 10.1016/S0301-4622(98)00226-9 |
0.368 |
|
| 2007 |
Chipot C, Mark AE, Pande VS, Simonson T. Applications of free energy calculations to chemistry and biology Springer Series in Chemical Physics. 86: 463-501. DOI: 10.1007/978-3-540-38448-9_13 |
0.372 |
|
| 2006 |
Aleksandrov A, Simonson T. The tetracycline: Mg2+ complex: a molecular mechanics force field. Journal of Computational Chemistry. 27: 1517-33. PMID 16847933 DOI: 10.1002/Jcc.20453 |
0.473 |
|
| 2006 |
Thompson D, Simonson T. 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. The Journal of Biological Chemistry. 281: 23792-803. PMID 16774919 DOI: 10.1074/Jbc.M602870200 |
0.485 |
|
| 2006 |
Thompson D, Plateau P, Simonson T. Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase. Chembiochem : a European Journal of Chemical Biology. 7: 337-44. PMID 16408313 DOI: 10.1002/Cbic.200500364 |
0.452 |
|
| 2006 |
Calimet N, Simonson T. Cys(x)His(y)-Zn2+ interactions: possibilities and limitations of a simple pairwise force field. Journal of Molecular Graphics & Modelling. 24: 404-11. PMID 16298534 DOI: 10.1016/J.Jmgm.2005.10.006 |
0.493 |
|
| 2005 |
Archontis G, Simonson T. A residue-pairwise generalized born scheme suitable for protein design calculations. The Journal of Physical Chemistry. B. 109: 22667-73. PMID 16853951 DOI: 10.1021/Jp055282+ |
0.438 |
|
| 2005 |
Simonson T. [The < folding problem >: can one predict the structure of proteins?]. Medecine Sciences : M/S. 21: 609-12. PMID 15985203 DOI: 10.1051/Medsci/2005216-7609 |
0.375 |
|
| 2005 |
Archontis G, Simonson T. Proton binding to proteins: a free-energy component analysis using a dielectric continuum model. Biophysical Journal. 88: 3888-904. PMID 15821163 DOI: 10.1529/Biophysj.104.055996 |
0.537 |
|
| 2004 |
Simonson T, Carlsson J, Case DA. Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models. Journal of the American Chemical Society. 126: 4167-80. PMID 15053606 DOI: 10.1021/Ja039788M |
0.492 |
|
| 2003 |
Moulinier L, Case DA, Simonson T. Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum. Acta Crystallographica. Section D, Biological Crystallography. 59: 2094-103. PMID 14646067 DOI: 10.1107/S090744490301833X |
0.382 |
|
| 2003 |
Simonson T. Electrostatics and dynamics of proteins Reports On Progress in Physics. 66: 737-787. DOI: 10.1088/0034-4885/66/5/202 |
0.416 |
|
| 2002 |
Simonson T, Calimet N. Cys(x)His(y)-Zn2+ interactions: thiol vs. thiolate coordination. Proteins. 49: 37-48. PMID 12211014 DOI: 10.1002/Prot.10200 |
0.434 |
|
| 2002 |
Simonson T, Archontis G, Karplus M. Free energy simulations come of age: protein-ligand recognition. Accounts of Chemical Research. 35: 430-7. PMID 12069628 DOI: 10.1021/Ar010030M |
0.467 |
|
| 2002 |
Simonson T. Gaussian fluctuations and linear response in an electron transfer protein. Proceedings of the National Academy of Sciences of the United States of America. 99: 6544-9. PMID 12011418 DOI: 10.1073/Pnas.082657099 |
0.417 |
|
| 2002 |
Nina M, Simonson T. Molecular Dynamics of the tRNAAla Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments Journal of Physical Chemistry B. 106: 3696-3705. DOI: 10.1021/Jp013855M |
0.399 |
|
| 2001 |
Archontis aG, Simonson T. Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model. Journal of the American Chemical Society. 123: 11047-11056. PMID 11686711 DOI: 10.1021/Ja010716+ |
0.453 |
|
| 2001 |
Calimet N, Schaefer M, Simonson T. Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins. 45: 144-158. PMID 11562944 DOI: 10.1002/Prot.1134 |
0.495 |
|
| 2001 |
Simonson T. Macromolecular electrostatics: continuum models and their growing pains. Current Opinion in Structural Biology. 11: 243-252. PMID 11297935 DOI: 10.1016/S0959-440X(00)00197-4 |
0.482 |
|
| 2001 |
Archontis G, Simonson T, Karplus M. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. Journal of Molecular Biology. 306: 307-27. PMID 11237602 DOI: 10.1006/Jmbi.2000.4285 |
0.524 |
|
| 2001 |
Höfinger S, Simonson T. Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time‐dependent charges Journal of Computational Chemistry. 22: 290-305. DOI: 10.1002/1096-987X(200102)22:3<290::Aid-Jcc1002>3.0.Co;2-V |
0.46 |
|
| 2000 |
Simonson T. Electrostatic Free Energy Calculations for Macromolecules: A Hybrid Molecular Dynamics/Continuum Electrostatics Approach Journal of Physical Chemistry B. 104: 6509-6513. DOI: 10.1021/Jp0014317 |
0.421 |
|
| 1999 |
Simonson T, Archontis G, Karplus M. A Poisson−Boltzmann Study of Charge Insertion in an Enzyme Active Site: The Effect of Dielectric Relaxation The Journal of Physical Chemistry B. 103: 6142-6156. DOI: 10.1021/Jp991354J |
0.469 |
|
| 1999 |
Wagner F, Simonson T. Implicit Solvent Models: Combining an Analytical Formulation of Continuum Electrostatics with Simple Models of the Hydrophobic Effect Journal of Computational Chemistry. 20: 322-335. DOI: 10.1002/(Sici)1096-987X(199902)20:3<322::Aid-Jcc4>3.0.Co;2-Q |
0.492 |
|
| 1998 |
Arnez JG, Flanagan K, Moras D, Simonson T. Engineering an Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments. Proteins. 32: 362-80. PMID 9715912 DOI: 10.1002/(Sici)1097-0134(19980815)32:3<362::Aid-Prot11>3.0.Co;2-7 |
0.408 |
|
| 1998 |
Zeng J, Treutlein HR, Simonson T. Conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations. Proteins. 31: 186-200. PMID 9593192 DOI: 10.1002/(Sici)1097-0134(19980501)31:2<186::Aid-Prot8>3.0.Co;2-K |
0.473 |
|
| 1998 |
Archontis G, Simonson T, Moras D, Karplus M. Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations. Journal of Molecular Biology. 275: 823-46. PMID 9480772 DOI: 10.1006/Jmbi.1997.1470 |
0.543 |
|
| 1998 |
Simonson T. Dielectric Constant Of Cytochrome C From Simulations In A Water Droplet Including All Electrostatic Interactions Journal of the American Chemical Society. 120: 4875-4876. DOI: 10.1021/Ja980071M |
0.325 |
|
| 1997 |
Simonson T, Perahia D. Polar fluctuations in proteins: molecular-dynamic studies of cytochrome c in aqueous solution. Faraday Discussions. 71-90. PMID 9136636 DOI: 10.1039/Fd9960300071 |
0.377 |
|
| 1997 |
Simonson T, Archontis G, Karplus M. Continuum Treatment of Long-Range Interactions in Free Energy Calculations. Application to Protein−Ligand Binding. The Journal of Physical Chemistry B. 101: 8349-8362. DOI: 10.1021/Jp9711499 |
0.431 |
|
| 1997 |
Simonson T, Wong CF, Brünger AT. Classical and Quantum Simulations of Tryptophan in Solution Journal of Physical Chemistry A. 101: 1935-1945. DOI: 10.1021/Jp962810W |
0.47 |
|
| 1996 |
Simonson T. Accurate calculation of the dielectric constant of water from simulations of a microscopic droplet in vacuum Chemical Physics Letters. 250: 450-454. DOI: 10.1016/0009-2614(96)00058-9 |
0.354 |
|
| 1995 |
Simonson T, Perahia D. Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. Proceedings of the National Academy of Sciences of the United States of America. 92: 1082-6. PMID 7862638 DOI: 10.1073/Pnas.92.4.1082 |
0.411 |
|
| 1995 |
Hodel A, Rice LM, Simonson T, Fox RO, Brünger AT. Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations. Protein Science : a Publication of the Protein Society. 4: 636-54. PMID 7613463 DOI: 10.1002/Pro.5560040405 |
0.351 |
|
| 1995 |
Simonson T, Perahia D. Microscopic Dielectric Properties of Cytochrome c from Molecular Dynamics Simulations in Aqueous Solution Journal of the American Chemical Society. 117: 7987-8000. DOI: 10.1021/Ja00135A018 |
0.33 |
|
| 1995 |
Simonson T, Perahia D. Dielectric properties of proteins from simulations: tools and techniques Computer Physics Communications. 91: 291-303. DOI: 10.1016/0010-4655(95)00054-J |
0.375 |
|
| 1994 |
Simonson T, Bruenger AT. Solvation Free Energies Estimated from Macroscopic Continuum Theory: An Accuracy Assessment The Journal of Physical Chemistry. 98: 4683-4694. DOI: 10.1021/J100068A033 |
0.344 |
|
| 1993 |
Hodel A, Simonson T, Fox RO, Brünger AT. Conformational substates and uncertainty in macromolecular free energy calculations Journal of Physical Chemistry. 97: 3409-3417. DOI: 10.1021/J100115A054 |
0.42 |
|
| 1993 |
Hodel A, Simonson T, Fox RO, Brunger AT. Conformational substrates and uncertainty in macromolecular free energy calculations The Journal of Physical Chemistry. 97: 3409-3417. DOI: 10.1021/j100115a054 |
0.304 |
|
| 1992 |
Simonson T, Perahia D. Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk. Biophysical Journal. 61: 410-27. PMID 1547329 DOI: 10.1016/S0006-3495(92)81847-7 |
0.389 |
|
| 1992 |
Simonson T, Brünger AT. Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations. Biochemistry. 31: 8661-74. PMID 1390651 DOI: 10.1021/Bi00151A037 |
0.446 |
|
| 1991 |
Simonson T, Perahia D, Bricogne G. Intramolecular dielectric screening in proteins. Journal of Molecular Biology. 218: 859-86. PMID 2023253 DOI: 10.1016/0022-2836(91)90273-9 |
0.443 |
|
| 1991 |
Simonson T, Perahia D, Brünger AT. Microscopic theory of the dielectric properties of proteins. Biophysical Journal. 59: 670-90. PMID 1646659 DOI: 10.1016/S0006-3495(91)82282-2 |
0.394 |
|
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