LDM publications
Publications 2010
Hagiwara Y, Field MJ, Nureki O and Tateno M
Editing mechanism of aminoacyl-tRNA synthetases operates by a hybrid ribozyme/protein catalyst.
Journal of the American Chemical Society (2010) 132(8) : 2751-2758
Vaccaro L, Artero V, Canaguier S, Fontecave M and Field MJ
Mechanism of hydrogen evolution catalyzed by NiFe hydrogenases : insights from a Ni-Ru model compound.
Dalton Transactions (2010) 39(12) : 3043-3049
Publications 2009
Canaguier S, Vaccaro L, Artero V, Ostermann R, Pecaut J, Field MJ and Fontecave M
Cyclopentadienyl ruthenium-nickel catalysts for biomimetic hydrogen evolution : electrocatalytic properties and mechanistic DFT studies.
Chemistry-a European Journal (2009) 15(37) : 9350-9364
Lelimousin M, Adam V, Nienhaus GU, Bourgeois D and Field MJ
Photoconversion of the fluorescent protein EosFP : A hybrid potential simulation study reveals intersystem crossings.
Journal of the American Chemical Society (2009) 131(46) : 16814-16823
Miguet L, Zervosen A, Gerards T, Pasha F A, Luxen A, Distèche-Nguyen M and Thomas A
Discovery of new inhibitors of resistant /Streptococcus pneumoniae/ penicillin binding protein (PBP) 2x by structure-based virtual screening.
Journal of Medical Chemistry (2009) 52(19) : 5926-5936
Mugherli L, Burchak O N, Balakireva L A, Thomas A, Chatelain F and Balakirev M Y
In situ assembly and screening of enzyme inhibitors with surface-tension microarrays.
Angewandte Chemie International Edition England (2009) 48(41) : 7639-7644
Roy S, Goedecker S, Field MJ and Penev E
A minima-hopping study of all-atom protein folding and structure prediction.
Journal of Physical Chemistry B (2009) 113(20) : 7315-7321
Publications 2008
Adam V, Lelimousin M, Boehme S, Desfonds G, Nienhaus K, Field MJ, Wiedenmann J, McSweeney S, Nienhaus GU and Bourgeois D
Structural characterization of IrisFP, an optical highlighter undergoing multiple photo-induced transformations.
Proceeding of the National Academy of Sciences U S A (2008) 105(47) : 18343-18348
Fdez Galvan I, Volbeda A, Fontecilla-Camps JC and Field MJ
A QM/MM study of proton transport pathways in a [NiFe] hydrogenase.
Proteins (2008) 73(1) : 195-203
Galvan IF and Field MJ
Improving the efficiency of the NEB reaction path finding algorithm.
Journal of Computational Chemistry (2008) 29(1) : 139-143
Publications 2007
Amara P, Fdez Galvan I, Fontecilla-Camps JC and Field MJ
The enamine intermediate may not be universal to thiamine catalysis.
Angewandte Chemie International Edition England (2007) 46(47) : 9019-9022
Crehuet R and Field MJ
A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase.
Journal of Physical Chemistry B (2007) 111(20) : 5708-5718
Fioravanti E, Vellieux FM, Amara P, Madern D and Weik M
Specific radiation damage to acidic residues and its relation to their chemical and structural environment.
Journal of synchrotron radiation (2007) 14(Pt 1) : 84-91
Katona G, Carpentier P, Niviere V, Amara P, Adam V, Ohana J, Tsanov N and Bourgeois D
Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.
Science (2007) 316(5823) : 449-453
Lepsik M and Field MJ
Binding of calcium and other metal ions to the EF-Hand loops of calmodulin studied by quantum chemical calculations and molecular dynamics simulations.
Journal of Physical Chemistry B (2007) 111(33) : 10012-10022
Puig E, Garcia-Viloca M, Gonzalez-Lafont A, Lluch JM and Field MJ
New Insights into the reaction mechanism catalyzed by the glutamate racemase enzyme : pH titration curves and classical molecular dynamics simulations.
Journal of Physical Chemistry B (2007) 111(9) : 2385-2397
Publications 2006
Amara P and Serre L
Functional flexibility of Bacillus stearothermophilus formamidopyrimidine DNA-glycosylase.
DNA Repair (2006) 5(8) : 947-958
Suarez D, Diaz N, Fontecilla-Camps J and Field MJ
A Computational Study of the Deacylation Mechanism of Human Butyrylcholinesterase.
Biochemistry (2006) 45(24) : 7529-7543
Thomas A and Field MJ
A comparative QM/MM simulation study of the reaction mechanisms of human and Plasmodium falciparum HG(X)PRTases.
Journal of the American Chemical Society (2006) 128(31) : 10096-10102
Publications 2005
Amara P, Volbeda A, Fontecilla-Camps JC and Field MJ
A quantum chemical study of the reaction mechanism of acetyl-coenzyme a synthase
Journal of the American Chemical Society (2005) 127(8) : 2776-2784
Crehuet R, Thomas A and Field MJ
An implementation of the nudged elastic band algorithm and application to the reaction mechanism of HGXPRTase from Plasmodium falciparum
Journal of Molecular Graphics and Modelling (2005) 24(2) : 102-110
Suarez D and Field MJ
Molecular dynamics simulations of human butyrylcholinesterase
Proteins : structure, function and bioinformatics (2005) 59(1) : 104-117
Publications 2004
Amara P, Serre L, Castaing B and Thomas A
Insights into the DNA repair process by the formamido-pyriminide-DNA glycosylase investigated by molecular dynamics
Protein Science (2004) 13 : 2009-2021
Crehuet R, Field M J and Pellegrini E
Transition events in one dimension - art. no. 012101.
Physical Review E (2004) 6901(1) Part 1) : NIL_547-NIL_550
Diaz N and Field M J
Insights into the Phosphoryl-Transfer Mechanism of cAMP-Dependent Protein Kinase from Quantum Chemical Calculations and Molecular Dynamics Simulations.
Journal of the American Chemical Society (2004) 126(2) : 529-42
Rinaldo D and Field MJ
A density functional theory study of the iron-binding site of human serum transferrin
Australian Journal of Chemistry (2004) 57(12) : 1219-1222
Rinaldo D, Vita C and Field M J
Engineering strontium binding affinity in an EF-Hand motif : a quantum chemical and molecular dynamics study
Journal of Biomolecular Structure and Dynamics (2004) 22(3) : 281-298
Publications 2003
Amara P and Field M J
Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method
Theoretical Chemistry Accounts (2003) 109(1) : 43-52
Crehuet R and Field M J
Comment on "Action-derived molecular dynamics in the study of rare events" - art. no. 089801
Physical Review Letters (2003) 9008(8) : NIL_238
Crehuet R and Field M J
A temperature-dependent nudged-elastic-band algorithm
Journal of Chemical Physics (2003) 118(21) : 9563-9571
Field M J
La simulation de la structure et de la fonction des protéines et d’autres macromolécules biologiques
Clés CEA (2003) 47 : 34-38
Field M J (2003)
Simulating chemical reactions in complex systems in Handbook of Numarical Analysis, Vol X, edited by Bris L. Elsevier Science
Field M J, Rinaldo D and Thomas A
Comment fonctionnent les protéines ? La voie de la simulation
Biofutur (2003) 238 : 28-30
Oliva M, Dideberg O and Field M J
Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins : A molecular dynamics simulation study
Proteins Structure Function and Genetics (2003) 53(1) : 88-100
Pellegrini E and Field M J
Development and testing of a de novo drug-design algorithm
Journal of Computer Aided Molecular Design (2003) 17(10) : 621-41
Rinaldo D and Field M J
A computational study of the open and closed forms of the N-lobe human serum transferrin apoprotein
Biophysical Journal (2003) 85(6) : 3485-501
Wymore T, Deerfield D W, Field M J, Hempel J and Nicholas H B
Initial catalytic events in class 3 aldehyde deshydrogenase : MM and QM/MM simulations
Chemico-Biological Interactions (2003) 143/144 : 75-84
Publications 2002
Bret C, Roth M, Norager S, Hatchikian EC and Field MJ
Molecular Dynamics Study of Desulfovibrio africanus Cytochrome c(3) in Oxidized and Reduced Forms
Biophysical Journal (2002) 83(6) : 3049-65
David L, Amara P, Field M J and Major F
Parametrization of a force field for metals complexed to Biomacromolecules : applications to Fe(II), Cu(II) and Pb(II)
Journal of Computer Aided Molecular Design (2002) 16 : 635-651
Field MJ
Simulating enzyme reactions : Challenges and perspectives
Journal of Computational Chemistry (2002) 23(1) : 48-58
Pellegrini E and Field MJ
A generalized-born solvation model for macromolecular hybrid-potential calculations
Journal of Physical Chemistry A (2002) 106(7) : 1316-1326
Thomas A and Field MJ
Reaction Mechanism of the HGXPRTase from Plasmodiumfalciparum : A Hybrid Potential Quantum Mechanical/Molecular Mechanical Study
Journal of the American Chemical Society (2002) 124(42) : 12432-12438
Publications 2001
Amara, P., Andreoletti, P., Jouve, H. M. and Field, M. J.
Ligand diffusion in the catalase from Proteus mirabilis : A molecular dynamics study.
Protein Science (2001) 10(10) : 1927-1935
Field, M. J.
Molecular dynamics simulations with the MD-Grape Special Purpose Computer in Proceedings of the workshop on new horizons in computational science held in Tokyo, September, 1997. Ebisuzaki, T and Makino, J. Terra Scientific Publishing,(2001) : 133-142
Marti S, Andres J, Moliner V, Silla E, Tunon I, Bertran J and Field MJ
A hybrid potential reaction path and free energy study of the chorismate mutase reaction
Journal of the American Chemical Society(2001) 123(8) : 1709-1712
Roche O and Field M J
Theoretical study of the conformation of the lipoamide arm in a mutant H protein
Proteins (2001) 45(3) : 237-40
Publications 2000
Amara P, Field MJ, Alhambra C and Gao JL
The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations : formulation and tests of the analytical derivatives
Theoretical Chemistry Accounts (2000) 104(5) : 336-343
Bret C, Field MJ and Hemmingsen L
A chemical potential equalization model for treating polarization in molecular mechanical force fields
Molecular Physics (2000) 98(11) : 751-763
Field MJ, Albe M, Bret C, Proust-De Martin F and Thomas A
The Dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
Journal of Computational Chemistry (2000) 21(12) : 1088-1100
Hemmingsen L, Amara P, Ansoborlo E and Field MJ
Importance of charge transfer and polarization effects for the modeling of uranyl-cation complexes
Journal of Physical Chemistry A (2000) 104(17) : 4095-4101
Proust-De Martin, F., Dumas, R. and Field, M. J.
A hybrid potential free-energy study of the isomerization step of the acetohydroxy acid isomeroreductase reaction.
Journal of the American Chemical Society (2000) 122 : 7688-7697
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