Search - Archive ouverte HAL Access content directly

Filter your results

52 Results
authIdHal_s : pascal-auffinger

High temperature annealed molecular dynamics simulations as a tool for conformational sampling. Application to the bicyclic "222" cryptand

Pascal Auffinger , G. Wipff
Journal of Computational Chemistry, 1990, 11 (1), pp.19-31. ⟨10.1002/jcc.540110103⟩
Journal articles istex hal-03420380v1

Molecular dynamics simulations of nucleic acids

Pascal Auffinger , Eric Westhof
Wiley InterScience. Encyclopedia of Computational Chemistry, 5, 1998, Molecular modeling annual, ⟨10.1007/s0089490050141⟩
Book sections hal-03420761v1

The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

Pascal Auffinger , Lukasz Bielecki , Eric Westhof
Chemistry and Biology, 2003, 10 (6), pp.551-561. ⟨10.1016/S1074-5521(03)00121-2⟩
Journal articles hal-03420562v1

Location and distribution of modified nucleotides in tRNA

Pascal Auffinger , Henri Grosjean , Rob Benne
Modification and Editing of RNA, ASM Press, 1998, ⟨10.1128/9781555818296⟩
Book sections hal-03420771v1

Effects of pseudouridylation on tRNA hydration and dynamics: a theoretical approach

Pascal Auffinger , Eric Westhof
Modification and Editing of RNA, ASM Press, pp.103-112, 1998, ⟨10.1128/9781555818296.ch6⟩
Book sections hal-03420764v1

tRNA structure

Pascal Auffinger , Eric Westhof
Nature Publishing group. Encyclopedia of Life Sciences, 2001
Book sections hal-03838766v1

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⟩
Book sections hal-03811647v1

Hydrophobic Groups Stabilize the Hydration Shell of 2′-O-Methylated RNA Duplexes

Pascal Auffinger , Eric Westhof
Angewandte Chemie International Edition, 2001, 40 (24), pp.4648-4650. ⟨10.1002/1521-3773(20011217)40:24<4648::AID-ANIE4648>3.0.CO;2-U⟩
Journal articles istex hal-03420555v1

RNA tertiary structure

Pascal Auffinger , Eric Westhof
Meyers RA. Encyclopedia of Analytical Chemistry, Wiley & Sons Ltd, pp.5222-32, 2000
Book sections hal-03838735v1

Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study

Pascal Auffinger , Eric Westhof
Biophysical Chemistry, 2002, 95 (3), pp.203-210. ⟨10.1016/S0301-4622(01)00257-5⟩
Journal articles istex hal-03420557v1
Image document

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
Nucleic Acids Research, 1997, 25 (17), pp.3421-3427. ⟨10.1093/nar/25.17.3421⟩
Journal articles hal-03420489v1

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 of the American Chemical Society, 1996, 118 (5), pp.1181-1189. ⟨10.1021/ja952494j⟩
Journal articles istex hal-03420469v1

Water and ion binding around RNA and DNA (C,G) oligomers

Pascal Auffinger , Eric Westhof
Journal of Molecular Biology, 2000, 300 (5), pp.1113-1131. ⟨10.1006/jmbi.2000.3894⟩
Journal articles istex hal-03420543v1

RNA solvation: A molecular dynamics simulation perspective

Pascal Auffinger , Eric Westhof
Journal articles istex hal-03420540v1

Simulations of the molecular dynamics of nucleic acids

Pascal Auffinger , Eric Westhof
Current Opinion in Structural Biology, 1998, 8 (2), pp.227-236. ⟨10.1016/S0959-440X(98)80044-4⟩
Journal articles istex hal-03420501v1

H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations

Pascal Auffinger , E. Westhof
Biophysical Journal, 1996, 71 (2), pp.940-954. ⟨10.1016/S0006-3495(96)79298-6⟩
Journal articles hal-03420474v1

Hydrogens in RNA as visualized by molecular dynamics simulations

Pascal Auffinger , Andrea Vaina
Hydrogen- and hydration-sensitive structural Biology, 2005
Book sections hal-03811665v1

A simple test for evaluating the truncation effects in simulations of systems involving charged groups

Pascal Auffinger , David Beveridge
Chemical Physics Letters, 1995, 234 (4-6), pp.413-415. ⟨10.1016/0009-2614(95)00065-C⟩
Journal articles istex hal-03420457v1

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⟩
Book sections hal-03838787v1

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 istex hal-03420444v1

Water and ion binding around r(UpA)12and d(TpA)12Oligomers - comparison with RNA and DNA (CpG)12 duplexes

Pascal Auffinger , Eric Westhof
Journal of Molecular Biology, 2001, 305 (5), pp.1057-1072. ⟨10.1006/jmbi.2000.4360⟩
Journal articles istex hal-03420546v1

Molecular dynamics simulations of solvated yeast tRNA(Asp)

Pascal Auffinger , Shirley Louise-May , Eric Westhof
Biophysical Journal, 1999, 76 (1), pp.50-64. ⟨10.1016/S0006-3495(99)77177-8⟩
Journal articles hal-03420528v1

Molecular Dynamics Simulations of RNA Systems

Pascal Auffinger , Andrea C. Vaiana
Handbook of RNA biochemistry, 2005
Book sections hal-03811673v1

Hydration of C—H groups in tRNA

Pascal Auffinger , Shirley Louise-May , Eric Westhof
Faraday Discussions, 1996, 103, pp.151-173. ⟨10.1039/FD9960300151⟩
Journal articles istex hal-03420472v1

Rules governing the orientation of the 2′-hydroxyl group in RNA

Pascal Auffinger , Eric Westhof
Journal of Molecular Biology, 1997, 274 (1), pp.54-63. ⟨10.1006/jmbi.1997.1370⟩
Journal articles istex hal-03420485v1
Image document

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⟩
Book sections hal-03420750v1
Image document

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

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
RNA, 2019, 25 (2), pp.173-192. ⟨10.1261/rna.068437.118⟩
Journal articles hal-02119072v1
Image document

Deflating the RNA Mg2+ bubble. Stereochemistry to the rescue!

Pascal Auffinger , Eric Ennifar , Luigi d'Ascenzo
Preprints, Working Papers, ... hal-03018371v1
Image document

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