High temperature annealed molecular dynamics simulations as a tool for conformational sampling. Application to the bicyclic "222" cryptand
Pascal Auffinger
,
G. Wipff
Journal articles
istex
hal-03420380v1
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Molecular dynamics simulations of nucleic acids
Pascal Auffinger
,
Eric Westhof
Wiley InterScience.
Encyclopedia of Computational Chemistry , 5, 1998, Molecular modeling annual,
⟨10.1007/s0089490050141⟩
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hal-03420761v1
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The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations
Pascal Auffinger
,
Lukasz Bielecki
,
Eric Westhof
Journal articles
hal-03420562v1
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Location and distribution of modified nucleotides in tRNA
Pascal Auffinger
,
Henri Grosjean
,
Rob Benne
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hal-03420771v1
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Effects of pseudouridylation on tRNA hydration and dynamics: a theoretical approach
Pascal Auffinger
,
Eric Westhof
Book sections
hal-03420764v1
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tRNA structure
Pascal Auffinger
,
Eric Westhof
Nature Publishing group. Encyclopedia of Life Sciences , 2001
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hal-03838766v1
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Metal Ion Binding to RNA
Pascal Auffinger
,
Neena Grover
,
Eric Westhof
Structural and Catalytic Roles of Metal Ions in RNA , Royal Society of Chemistry, pp.1-36, 2011, Metal Ions in Life Sciences,
⟨10.1039/978184973251200001⟩
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hal-03811647v1
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Hydrophobic Groups Stabilize the Hydration Shell of 2′-O-Methylated RNA Duplexes
Pascal Auffinger
,
Eric Westhof
Journal articles
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hal-03420555v1
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RNA tertiary structure
Pascal Auffinger
,
Eric Westhof
Meyers RA. Encyclopedia of Analytical Chemistry , Wiley & Sons Ltd, pp.5222-32, 2000
Book sections
hal-03838735v1
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Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study
Pascal Auffinger
,
Eric Westhof
Journal articles
istex
hal-03420557v1
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Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme
Pascal Auffinger
,
Thomas Hermann
,
Scott G. Williams
,
Eric Westhof
Journal articles
hal-03420489v1
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Molecular Dynamics Simulations of the Anticodon Hairpin of tRNA(Asp) : Structuring Effects of C−H···O Hydrogen Bonds and of Long-Range Hydration Forces
Pascal Auffinger
,
Shirley Louise-May
,
Eric Westhof
Journal articles
istex
hal-03420469v1
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Water and ion binding around RNA and DNA (C,G) oligomers
Pascal Auffinger
,
Eric Westhof
Journal articles
istex
hal-03420543v1
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RNA solvation: A molecular dynamics simulation perspective
Pascal Auffinger
,
Eric Westhof
Journal articles
istex
hal-03420540v1
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Simulations of the molecular dynamics of nucleic acids
Pascal Auffinger
,
Eric Westhof
Journal articles
istex
hal-03420501v1
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H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations
Pascal Auffinger
,
E. Westhof
Journal articles
hal-03420474v1
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Hydrogens in RNA as visualized by molecular dynamics simulations
Pascal Auffinger
,
Andrea Vaina
Hydrogen- and hydration-sensitive structural Biology , 2005
Book sections
hal-03811665v1
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A simple test for evaluating the truncation effects in simulations of systems involving charged groups
Pascal Auffinger
,
David Beveridge
Journal articles
istex
hal-03420457v1
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Halogen interactions in biomolecular crystal structures
M. Vallejos
,
Pascal Auffinger
,
P. Ho
Arnold E, Himmel DM, Rossman MG.
International Tables for Crystallography , F (2), International Union of Crystallography; Wiley, pp.821-826, 2012,
⟨10.1107/97809553602060000895⟩
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hal-03838787v1
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Molecular dynamics simulations on the protonated 222. H+ and 222.2H+ cryptands in water: Endo versus exo conformations
Pascal Auffinger
,
G. Wipff
Journal of Inclusion Phenomena and Molecular Recognition in Chemistry , 1991, 11 (1), pp.71-88.
⟨10.1007/BF01073686⟩
Journal articles
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hal-03420444v1
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Water and ion binding around r(UpA)12and d(TpA)12Oligomers - comparison with RNA and DNA (CpG)12 duplexes
Pascal Auffinger
,
Eric Westhof
Journal articles
istex
hal-03420546v1
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Molecular dynamics simulations of solvated yeast tRNA(Asp)
Pascal Auffinger
,
Shirley Louise-May
,
Eric Westhof
Journal articles
hal-03420528v1
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Molecular Dynamics Simulations of RNA Systems
Pascal Auffinger
,
Andrea C. Vaiana
Handbook of RNA biochemistry , 2005
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hal-03811673v1
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Hydration of C—H groups in tRNA
Pascal Auffinger
,
Shirley Louise-May
,
Eric Westhof
Journal articles
istex
hal-03420472v1
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Rules governing the orientation of the 2′-hydroxyl group in RNA
Pascal Auffinger
,
Eric Westhof
Journal articles
istex
hal-03420485v1
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Treatment of counterions in computer simulations of DNA
Ganesan Ravishanker
,
Pascal Auffinger
,
David Langley
,
Bhyravabhotla Jayaram
,
Matthew Young
et al.
Reviews in Computational Chemistry , John Wiley & Sons, Inc., pp.317-372, 2007, Reviews in Computational Chemistry,
⟨10.1002/9780470125885.ch6⟩
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hal-03420750v1
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Multiscale Modelling of Phosphate…π Contacts in RNA U-turns Exposes Differences Between Quantum-ChemicalM and AMBER Force Field Descriptions
Klaudia Mráziková
,
Holger Kruse
,
Vojtěch Mlýnský
,
Pascal Auffinger
,
Jirí Sponer
et al.
Journal of Chemical Information and Modeling , In press
Journal articles
hal-03857441v1
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Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders—a critical PDB survey
Filip Leonarski
,
Luigi d'Ascenzo
,
Pascal Auffinger
Journal articles
hal-02119072v1
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Deflating the RNA Mg2+ bubble. Stereochemistry to the rescue!
Pascal Auffinger
,
Eric Ennifar
,
Luigi d'Ascenzo
2020
Preprints, Working Papers, ...
hal-03018371v1
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Structural and Dynamical Characterization of Nucleic Acid Water and Ion Binding Sites
Pascal Auffinger
,
Benoit Masquida
,
Eric Westhof
Computational Methods for Macromolecules: Challenges and Applications , 2002
Book sections
hal-03811682v1
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