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Publications

Examples of studies performed wholly or partially with fDynamo or pDynamo include:

  1. A. Thomas, D. Jourand, C. Bret, P. Amara and M. J. Field. Is There a Covalent Intermediate in the Viral Neuraminidase Reaction? A Hybrid-Potential Free-Energy Study. J. Am. Chem. Soc. 121, 9693–9702 (1999) [Link].
  2. C. Bret, M. J. Field and L. Hemmingsen. A Chemical Potential Equalization Model for Treating Polarization in Molecular Mechanical Force Fields. Mol. Phys. 98, 751–763 (2000) [Link].
  3. F. Proust-De Martin, R. Dumas and M. J. Field. A Hybrid-Potential Free-Energy Study of the Isomerization Step of the Acetohydroxy Acid Isomeroreductase Reaction. J. Am. Chem. Soc. 122, 7688–7697 (2000) [Link].
  4. S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán and M. J. Field. Insights into Enzyme Catalysis: The Chorismate Mutase Case. J. Am. Chem. Soc. 123, 1709–1712 (2001) [Link].
  5. E. Pellegrini and M. J. Field. A Generalized Born Solvation Model for Macromolecular Hybrid-Potential Calculations. J. Phys. Chem. A 106, 1316–1326 (2002) [Link].
  6. A. Thomas and M. J. Field. Reaction Mechanism of the HGXPRTase from Plasmodium falciparum: A Hybrid Potential Quantum Mechanical/Molecular Mechanical Study. J. Am. Chem. Soc. 124, 12432–12438 (2002) [Link].
  7. P. Amara and M. J. Field. Evaluation of an Ab Initio QM/MM Hybrid-Potential Link-Atom Method. Theor. Chem. Accts. 109, 43–52 (2003) [Link].
  8. T. Wymore, D. W. Deerfield II, M. J. Field, J. Hempel and H. B. Nicholas, Jr. Initial Catalytic Events in Class 3 Aldehyde Dehydrogenase: MM and QM/MM Simulations. Chemico-Biological Interactions 143/144, 75–84 (2003) [Link].
  9. M. Oliva, O. Dideberg and M. J. Field. Understanding the Molecular Mechanims of Active-Site Serine Penicillin-Recognizing Proteins: A Molecular Dynamics Simulations Study. Proteins: Structure, Function and Genetics 53, 88–100 (2003) [Link].
  10. E. Pellegrini and M. J. Field. Development and Testing of a de novo Drug-Design Algorithm. J. Comput. Aided Mol. Design 17, 621–41 (2003) [Link].
  11. N. Diaz and M. J. Field. Insights into the Phosphoryl-Transfer Mechanism of cAMP-Dependent Protein Kinase from Quantum Chemical Calculations and Molecular Dynamics Simulations. J. Am. Chem. Soc. 126, 529–542 (2004) [Link].
  12. T. Wymore, J. Hempel, S. S. Cho, A. D. MacKerell Jr., H. B. Nicholas Jr. and D. W. Deerfield II. Molecular Recognition of Aldehydes by Aldehyde Dehydrogenase and Mechanism of Nucleophile Activation. Proteins: Structure, Function and Genetics 57, 758–771 (2004) [Link].
  13. R. Crehuet, A. Thomas and M. J. Field. An Implementation of the Nudged-Elastic-Band Algorithm and Application to the Reaction Mechanism of HGXPRTase from Plasmodium Falciparum. J. Mol. Graph. Model. 24, 102–110 (2005) [Link].
  14. A. Thomas and M. J. Field. A Comparative QM/MM Simulation Study of the Reaction Mechanisms of Human and Plasmodium falciparum HG(X)PRTases. J. Am. Chem. Soc. 128, 10096–10102 (2006) [Link].
  15. G. M. Arantes and M. Loos. Specific Parametrisation of a Hybrid Potential to Simulate Reactions in Phosphatases. Phys. Chem. Chem. Phys. 8, 347–353 (2006) [Link].
  16. G. M. Arantes. Free-Energy Profiles for Catalysis by a Dual-Specificity Phosphatase. Biochemical Journal 399, 343-350 (2006) [Link].
  17. S. Keinan, X. Hu, D. N. Beratan and W. Yang. Designing Molecules with Optimal Properties using the Linear Combination of Atomic Potentials Approach in an AM1 Semiempirical Framework. J. Phys. Chem. A 111 176–181 (2007) [Link].
  18. R. Crehuet and M. J. Field. A Transition Path Sampling Study of the Reaction Catalyzed by the Enzyme Chorismate Mutase. J. Phys. Chem. B 111, 5708–5718 (2007) [Link].
  19. T. Wymore, D. W. Deerfield II and J. Hempel. Mechanistic Implications of the Cysteine-Nicotinamide Adduct in Aldehyde Dehydrogenase Based on Quantum Mechanical/Molecular Mechanical Simulations. Biochemistry 46, 9495–9506 (2007) [Link].
  20. P. Amara, I. Fernandez Galván, J. C. Fontecilla-Camps and M. J. Field. The Enamine Intermediate May Not Be Universal to Thiamine Catalysis. Angew. Chemie Intl. Ed. 46, 9019–9022 (2007) [Link].
  21. I. Fernandez Galván and M. J. Field. Improving the Efficiency of the NEB Reaction Path Finding Algorithm. J. Comp. Chem. 29, 2008, 139–143 (2008) [Link].
  22. I. Fernandez Galván, A. Volbeda, J. C. Fontecilla-Camps and M. J. Field. A QM/MM Study of Proton Transport Pathways in a Nickel-Iron Hydrogenase. Proteins: Structure, Function and Bioinformatics 73, 195–203 (2008) [Link].
  23. G. M. Arantes. The Catalytic Acid in the Dephosphorylation of the Cdk2-pTpY/CycA Protein Complex by Cdc25B Phosphatase. J. Phys. Chem. B 112, 1524415247 (2008) [Link].
  24. G. M. Arantes and M. C. C. Ribeiro. A Microscopic View of Substitution Reactions Solvated by Ionic Liquids. J. Chem. Phys. 128, 114503 (2008) [Link].
  25. S. Roy, S. Goedecker, M. J. Field and E. Penev. A Minima-Hopping Study of All-Atom Protein Folding and Structure Prediction. J. Phys. Chem. B 113, 7315–7321 (2009) [Link].
  26. M. Lelimousin, V. Adam, G. U. Nienhaus, D. Bourgeois and M. J. Field. Photoconversion of the Fluorescent Protein EosFP: A Hybrid Potential Simulation Study Reveals Intersystem Crossings. J. Am. Chem. Soc. 131, 16814–16823 (2009) [Link].
  27. E. Marcos, M. J. Field and R. Crehuet. Pentacoordinated Phosphorus Revisited by High-Level QM/MM Calculations. Proteins: Structure, Function and Bioinformatics 78, 2405–2411 (2010) [Link].
  28. A. Aleksandrov and M. J. Field. Efficient Solvent Boundary Potential for Hybrid Potential Simulations. Phys. Chem. Chem. Phys. 13, 10503-10509 (2011) [Link].
  29. A. Roy, M. J. Field, V. Adam and D. Bourgeois. The Nature of Transient Dark States in a Photoactivatable Fluorescent Protein. J. Am. Chem. Soc. 133, 18586–18589 (2011) [Link].
  30. A. Aleksandrov and M. J.Field. A Hybrid Elastic Band String Algorithm for Studies of Enzymatic Reactions. Phys. Chem. Chem. Phys. 14, 12544-12553 (2012) [Link].
  31. A. Baggioli, O. Crescenzi, M. J. Field, F. Castiglione and G. Raos. Computational 17O-NMR Spectroscopy of Organic Acids and Peracids: Comparison of Solvation Models. Phys. Chem. Chem. Phys. 15, 1130-1140 (2013) [Link].
  32. M. Feliks, B. M. Martins and G. M. Ullmann. Catalytic Mechanism of the Glycyl Radical Enzyme 4-Hydroxyphenylacetate Decarboxylase from Continuum Electrostatic and QC/MM Calculations. J. Am. Chem. Soc. 135, 14574-14585 (2013) [Link].
  33. A. Aleksandrov and M. J. Field. Mechanism of Activation of Elongation Factor Tu by Ribosome: Catalytic Histidine Activates GTP by Protonation. RNA 19, 1218-1225 (2013) [Link].
  34. G.M. Arantes, A. Bhattacharjee and M. J. Field. Homolytic Cleavage of FeS Bonds in Rubredoxin under Mechanical Stress. Angew. Chem. Int. Ed. 52, 8144-8146 (2013) [Link].
  35. M. Sanchez-Martinez, E. Marcos, R. Tauler, M. J. Field and R. Crehuet. Conformational Compression and Barrier Height Heterogeneity in the N-Acetylglutatmate Kinase. J. Phys. Chem. B (2013) [Link].