Pascal Auffinger: publication list and Curriculum Vitae

 

2011

 

  • AUFFINGER P, GROVER N & WESTHOF E (2011)
    Metal ion binding to RNA.
    In “Structural and Catalytic Roles of Metal Ions in RNA”,
    (Sigel A, Sigel H & Sigel RKO eds), The Royal Society of Chemistry, Cambridge, UK, Vol. 9 of "Metals in Life Sciences" pp. 1-35. (PDF local)
  • VALLEJOS MJ, AUFFINGER P & HO PS (2011)
    Molecular halogen interactions in biomolecular crystal structures.
    In “International Tables of Crystallography”,
    (Arnold E, Himmel DM & Rossman MG eds), Chichester, Willey, Vol. F of "Crystallography of Biological Macromolecules, 2nd ed." ch. 23.6. (edited PDF local)

2009

 

  • HASHEM Y & AUFFINGER P (2009)
    A short guide formolecular dynamics simulations of RNA systems.
    Methods, 47, 187-97. (Abstract) - (PDF local)

2008

 

  • AUFFINGER P, WESTHOF E & HASHEM Y (2008)
    Milestones in RNA molecular dynamics simulations.
    In “Computational structural biology”,
    (Schwede T & Peitsch M eds), World Scientific Publishing Co, pp. 363-99. (PDF local)

2007

 

  • AUFFINGER P, CHEATHAM TE III & VAIANA AC (2007)
    Spontaneous formation of KCl aggregates in biomolecular simulations: a force field issue?
    J. Chem. Theory Comput., 3, 379-88. (Abstract) - (PDF local) (Supplementary material)
  • AUFFINGER P & HASHEM Y (2007)
    SwS: a solvation web service for nucleic acids.
    Bioinformatics, 23, 1035-7. (Abstract) - (PDF local)
    SwS: Solvation web Service for nucleic acids
  • SANTINI GPH, PAKLEZA C, AUFFINGER P, CELINE M, FAVRE A, CLIVIO P & COGNET JAH (2007)
    Dinucleotide TpT and its 2’O-Me analogue possess different backbone conformations and flexibilities but similar stacked geometries.
    J. Phys. Chem. B, 111, 9400-9. (Abstract) - (PDF local)
  • AUFFINGER P & HASHEM Y (2007)
    Nucleic acid solvation: from outside to insight.
    Curr. Op. Struct. Biol., 17, 325-33. (Abstract) - (PDF local)

2006

 

  • VAIANA AC, WESTHOF E & AUFFINGER P (2006)
    A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns.
    Biochimie, 88, 1061-73. (Abstract) - (PDF local)
  • AUFFINGER P (2006)
    Molecular dynamics simulations of RNA systems: importance of the initial conditions.
    In “Computational studies of DNA and RNA”,
    (Sponer J & Lankas F eds), Springer Verlag, Berlin, pp. 283-300. (PDF local)

2005


  • AUFFINGER P & VAIANA AC (2005)
    Hydrogen in RNA as visualized by molecular dynamics simulations.
    In "Hydrogen- and Hydration-Sensitive Structural Biology",
    (Niimura N.Mizuno H, Helliwell J & Westhof E eds), KubaPro Co. Ltd., Tokyo, pp. 227-34. (PDF local)
  • AUFFINGER P & VAIANA AC (2005)
    Molecular dynamics simulations of RNA systems.
    In "Handbook of RNA Biochemistry",
    (Hartmann RK, Bindereif A, Schön A & Westhof E eds), Wiley-VCH Verlag, Weinheim, pp. 560-76. (PDF local)

2004


  • AUFFINGER P, BIELECKI L & WESTHOF E (2004)
    Anion binding to nucleic acids.
    Structure, 12, 379-88. (Abstract) - (PDF local)
  • AUFFINGER P, BIELECKI L & WESTHOF E (2004)
    Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations.
    J. Mol. Biol., 335, 555-71 (Abstract) - (PDF local)
  • AUFFINGER P, HAYS HA, WESTHOF E & HO PS (2004)
    Halogen bonds in biological structures.
    Proc. Natl. Acad. Sci., USA, 101, 16789-94. (Abstract) - (PDF local) - (Supplementary material)

2003


  • AUFFINGER P, BIELECKI L & WESTHOF E (2003)
    The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations.
    Chem. Biol., 10, 551-61. (PDF) - (Supplementary material)

2002


  • AUFFINGER P & WESTHOF E (2002)
    Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study.
    Biophys. Chem., 95, 203-10. (PDF local)
  • AUFFINGER P, MASQUIDA M & WESTHOF E (2002)
    Strucutral and dynamical characterization of nucleic acids water and ion binding sites.
    In "Computational methods for macromolecules: challenges and applications. - Proceedings of the 3rd international workshop on algorithms for macromolecular modeling, New York, October 12-14, 2000" Lecture Notes in Computational Science and Engineering,
    (Schlick T & Gan, HH eds), Springer Verlag. Vol. 24, pp. 61-70. (PDF local)

2001


  • AUFFINGER P & WESTHOF E (2001)
    Hydrophobic groups stabilize the hydration shell of 2'-O-methylated RNA duplexes.
    Angew. Chem. Int. Ed., 40, 4648-50. (PDF local) - (Supplementary material)
  • AUFFINGER P & WESTHOF E (2001)
    An extended structural signature for the tRNA anticodon loop.
    RNA, 7, 334-41. (PDF local)
  • AUFFINGER P & WESTHOF E (2001)
    Water and ion binding around r(UpA)12 and d(ApT)12 oligomers - Comparison with RNA and DNA (CpG)12 duplexes.
    J. Mol. Biol., 305, 1057-72. (PDF local) - (Supplementary material)
  • WESTHOF E & AUFFINGER P (2001)
    tRNA structure.
    In "Encyclopedia of Life Sciences",
    www.els.net, Nature Publishing Group. (PDF local)

2000


  • AUFFINGER P & WESTHOF E (2000)
    Water and ion binding around RNA and DNA (C,G) oligomers.
    J.Mol.Biol., 300, 1113-31. (PDF local)
  • WESTHOF E & AUFFINGER P (2000)
    RNA tertiary structure.
    In "Encyclopedia of Analytical Chemistry",
    (Meyers, RA, ed), John Wiley & Sons Ltd, Chichester, pp. 5222-32. (PDF local)
  • AUFFINGER P & WESTHOF E (2000)
    RNA solvation: a molecular dynamics simulation perspective.
    Biopolymers, 56, 266-74. (PDF local)

1999


  • AUFFINGER P, LOUISE-MAY S & WESTHOF E (1999)
    Molecular dynamics simulations of the solvated yeast tRN
    Asp.
    Biophys. J., 76, 50-64. (PDF local)
  • AUFFINGER P & WESTHOF E (1999)
    Singly and bifurcated Hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes.
    J. Mol. Biol., 292, 467-83. (PDF local)
  • AUFFINGER P & WESTHOF E (1999)
    Conformational preferences in RNA molecules as inferred from molecular dynamics simulations.
    In "Perspectives in Structural Biology. A Volume in Honour of G. N. Ramachandran",
    (Vijayan M, Yathidra N and Kolaskar AS, eds), Universities Press (India), Hyderabad, pp. 545-55. (PDF local)
  • AUFFINGER P & WESTHOF E (1999)
    Roles of hydration on the structure and dynamics of nucleic acids.
    In "ISOPOW 1998 Symposium. - Water management in the design and distribution of food."
    (Roos YH, Leslie RB & Lillford PJ, eds), Technomic Press, Basel, pp.165-98. (PDF lcoal)

1998


  • AUFFINGER P & WESTHOF E (1998)
    Hydration of RNA base bairs.
    "Dedicated to David Beveridge on the occasion of his 60th birthday"

    J. Biomol. Struct. Dyn., 16, 693-707. (PDF local)
  • HERMANN T, AUFFINGER P & WESTHOF E (1998)
    Molecular dynamics investigations of hammerhead ribozyme RNA.
    Eur. Biophys. J., 27, 153-65. (PDF lcoal)
  • AUFFINGER P & WESTHOF E (1998)
    Effects of pseudouridylation on tRNA hydration and dynamics: a theoretical approach.
    In "Modification and Editing of RNA",
    (Grosjean H & Benne R eds), ASM Press, Washington DC, pp. 103-12. (PDF local)
  • AUFFINGER P & WESTHOF E (1998)
    Appendix 5: location and distribution of modified nucleotides in tRNA.
    In "Modification and Editing of RNA",
    (Grosjean H & Benne R eds), ASM Press, Washington DC, pp. 569-76. (PDF local)
  • AUFFINGER P & WESTHOF E (1998)
    Molecular Dynamics: simulations of Nucleic Acids.
    In "Encyclopedia of computational chemistry",
    (Schleyer PvR ed), Wiley and Sons., Vol. 5, pp. 1629-40. (PDF local)
  • AUFFINGER P & WESTHOF E (1998)
    Simulations of the molecular dynamics of nucleic acids.
    Curr.Opin. Struct. Biol., 8, 227-36. (PDF local)

1997


  • AUFFINGER P & WESTHOF E (1997)
    RNA hydration: 3 nanoseconds of multiple molecular dynamics simulations of the solvated tRNAAsp anticodon hairpin.
    J. Mol. Biol., 269, 326-41. (PDF local)
  • AUFFINGER P & WESTHOF E (1997)
    Rules governing the orientation of the 2'-hydroxyl group in RNA.
    J. Mol. Biol., 274, 54-63. (PDF local)
  • HERMANN T, AUFFINGER P, SCOTT WG & WESTHOF E (1997)
    Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.
    Nucl. Acids Res., 25, 3421-7. (PDF local)
  • RAVISHANKER G, AUFFINGER P, LANGLEY DR, JAYARAM B, YOUNG MA & BEVERIDGE DL (1997)
    Treatment of counterions in computer simulations of DNA.
    In "Reviews of Computational Chemistry",
    (Lipkowitz KB & Boyd DB eds), VCH Publishers, Vol. 11, pp. 317-72. (PDF local)
  • WESTHOF E, AUFFINGER P & GASPIN C (1997)
    DNA and RNA structure prediction.
    In "DNA and Protein Sequence Analysis: A Practical Approach",
    (Bishop M & Rawlings C eds), IRL Press, Oxford, Vol. 14, pp. 255-78. (PDF local)

1996


  • AUFFINGER P & WESTHOF E (1996)
    H-bond stability in the tRNAAsp anticodon hairpin: 3 ns of multiple molecular dynamics simulations.
    Biophys. J., 71, 940-54 (PDF local)
  • AUFFINGER P, LOUISE-MAY S & WESTHOF E (1996)
    Hydration of C-H groups in tRNA.
    Faraday Discuss., 103, 151-73. (PDF local)
  • AUFFINGER P, LOUISE-MAY S & WESTHOF E (1996)
    Molecular dynamics simulations of the anticodon hairpin of tRNAAsp: Structuring effects of C-H...O hydrogen bonds and of long-range hydration forces.
    J. Am. Chem. Soc., 118, 1181-9. (PDF local)
  • LOUISE-MAY S, AUFFINGER P & WESTHOF E (1996)
    Calculations of nucleic acid conformations.
    Curr. Opin. Struct. Biol., 6, 289-98. (PDF local)
  • LOUISE-MAY S, AUFFINGER P & WESTHOF E (1996)
    RNA structure from molecular dynamics simulations.
    In "Biological Structure and Dynamics. Proceedings of the Ninth Conversation",
    (Sarma RH & Sarma MH eds), Adenine Press, State University of New-York, Albany NY, pp. 73-90. (PDF local)

1995


  • AUFFINGER P & BEVERIDGE DL (1995)
    A simple test for evaluating the truncation effects in simulation of systems involving charged groups.
    Chem. Phys. Lett., 234, 413-5. (PDF local)
  • AUFFINGER P, LOUISE-MAY S & WESTHOF E (1995)
    Multiple molecular dynamics simulations of the anticodon loop of tRNAAsp in aqueous solution with counterions.
    J. Am. Chem. Soc., 117, 6720-6. (PDF local)

1991


  • AUFFINGER P & WIPFF G (1991)
    Hydration of the "222" cryptand and cryptates studied by molecular dynamics simulations.
    J. Am. Chem. Soc., 113, 5976-88. (PDF local)
  • AUFFINGER P & WIPFF G (1991)
    Molecular Dynamics simulations on the protonated 222,H+ and 222,2H+ cryptands in water. Endo versus exo conformations.
    J. Incl. Phenom., 11, 71-81. (PDF local)
  • AUFFINGER P & WIPFF G (1991)
    Quantitative studies on molecular recognition: free energy perturbation studies on M+/222 cryptates in water and in methanol.
    J. Chim. Phys. Phys.-Chim. Biol., 88, 2525-34. (PDF local)

1990


  • AUFFINGER P & WIPFF G (1990)
    High temperature annealed molecular dynamics simulations as a tool for conformational sampling. Application to the bicyclic "222" cryptand.
    J. Comp. Chem., 11, 19-31. (PDF local)

Architecture et Réactivité de L'ARN

CNRS - UPR 9002