Some references

Observation (dating from 18/05): This bibliography is not complete. All participants are quite welcome to send me other references should they wish to (or pointers to programs or web pages). Just send them to me at the address: sagot@pasteur.fr. Thanks in advance.

Auffinger P., Westhof E. (1997) RNA hydration : 3 nanoseconds of multiple molecular dynamics simulations of the solvated tRNAAsp anticodon hairpin. J. Mol. Biol. 269:326-341.

Auffinger P., Westhof E. (1997) Rules governing the orientation of the 2'-hydroxyl group in RNA. J. Mol. Biol. 274:54-63.

Auffinger P., Louise-May S., Westhof E. (1999) Molecular dynamics simulations of the solvated yeast tRNAAsp. Biophysical Journal 76:50-64.

Chanfreau G., Abou Elela S., Ares M., Guthrie C. (1997) Alternative 3'-end processing of U5 snRNA by RNase III. Genes Dev. 11:2741-2751.

Chanfreau G., Legrain P., Jacquier A. (1998) Yeast RNase III as a key processing enzyme in nucleolar RNA metabolism. J. Mol. Biol. 284:975-988.

Chanfreau G., Rotondo G., Legrain P., Jacquier A. (1998) Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1. EMBO J. 17:3726-3737.

Chang K. Y, Varani G. (1997) Nucleic acids structure and recognition. Nat. Struct. Biol. 4(Suppl):854-858.

Corpet F., Michot B. (1994) RNAlign program: alignment of RNA sequences using both primary and secondary structures. Comput. Appl. Biosci. 10:389-399.

Gultyaev A.P., van Batenburg F.H.D., Pleij C.W.A. (1995) The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:37-51.

Gultyaev A.P., van Batenburg F.H.D., Pleij C.W.A. (1995) The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics. Nucleic Acid Res. 23:3718-3725.

Gultyaev A.P., van Batenburg F.H.D., Pleij C.W.A. (1998) Dynamic competition between alternative structures in viroid RNAs simulated by an RNA folding algorithm. J. Mol. Biol. 276:43-55.

Hermann T., Westhof E. (1998) Aminoglycoside binding to the hammerhead ribozyme : a general model for the interaction of cationic antibiotics with RNA. J. Mol. Biol. 276:903-912.

Hermann T., Westhof E. (1998) Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations. Structure 6:1303-1314.

Hermann T., Westhof E. (1998) Docking of cationic antibiotics to negatively charge d pockets in RNA folds. J. Medicinal Chemistry 42:1250-1261.

Hofacker I. L., Peter F. Stadler (1999) Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. Comp & Chem., 23:401-414.

Hofacker I. L. (1998) RNA Secondary Structures: A Tractable Model of Biopolymer Folding. In Monte Carlo Approach to Biopolymers and Protein Folding, Grassberger P., Barkema G., Nadler W. (eds.), World Scientific, Singapore.

Hofacker I. L., Schuster P. S., Stadler P. F. (1998) Combinatorics of RNA Secondary Structures. Discr. Appl. Math. 88: 207-237.

Hofacker I. L., Fekete M., Flamm C., Huynen M. A., Rauscher S., Stolorz P. E., Stadler P. F. (1998) Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes. Nucleic Acids Res. 26:3825-3836.

Kolk M.H., van der Graaf M., Wijmenga S.S., Pleij C.W.A., Heus H.A., Hilbers C.W. (1998) NMR structure of a classical pseudoknot: Interplay of single- and double-stranded RNA. Science 280:434-438.

Lehnert V., Jaeger L., Michel F., Westhof E. (1996) New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymen a thermophila ribozyme. Chemistry & Biology 3:993-1009.

Leontis N.B., Westhof E. (1998) The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure. RNA 4:1134-1153.

Leontis N.B., Westhof E. (1998) A common motif organizes the structure of multi-helix loops in 16S and 23S ribosomal RNAs. J. Mol. Biol. 283:571-583.

Massire C., Jaeger L., Westhof E. (1996) Derivation of the 3D architecture of bacterial RNAse P from comparative sequence analysis. J. Mol. Biol. 279:773-793.

Mathews D. H., Sabina J., Zuker M., Turner D. H. (1999) Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure. J. Mol. Biol. 288:911-940.

Melchers W.J.G., Hoenderop J.G.J., Slot H.J.B., Pleij C.W.A., Pilipenko E.V., Agol V.I., Galama J.M.D. (1997) Kissing of the two predominant hairpin loops in the coxsackie B virus 3' untranslated region is the essential structural feature of the origin of replication required for negative-strand RNA synthesis. J. Virol. 71:686-696.

Michel F., Westhof E. (1990) Modelling of the three-dimensional architecture of Group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:585-610.

Pleij C.W.A. (1995) Structure and Function of RNA Pseudoknots. Genet. Eng. P. 17:67-80.

Poot R.A., Pleij C.W.A., van Duin J. (1996) The central pseudoknot in 16S ribosomal RNA is needed for ribosome stability but is not essential for 30S initiation complex formation. Nucleic Acid Res. 24:3670-3676.

Poot R.A., van den Worm S.H.E., Pleij C.W.A., van Duin J. (1998) Base complementarity in helix 2 of the central pseudoknot in 16S rRNA is essential for ribosome functioning. Nucleic Acid Res. 26:549-553.

Tacker M., Stadler P. F., Bornberg-Bauer E. G., Hofacker I. L., Schuster P. (1996) Algorithm Independent Properties of RNA Secondary Structure Predictions. Eur. Biophy. J. 25:115-130.

ten Dam E.B., Verlaan P.W.G., Pleij C.W.A. (1995) Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: Loop lengths and stability of the stem regions. RNA 1:146-154.

Turner D. H. (1996) Thermodynamics of base pairing. Curr. Opin Struct. Biol. 6:299-304.

SantaLucia J. Jr., Turner D. H. (1997) Measuring the thermodynamics of RNA secondary structure formation. Biopolymers 44:309-319.

van Batenburg F.H.D., Gultyaev A.P., Pleij C.W.A. (1995) An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J. Theor. Biol. 174:269-280.

Varani G., Nagai K. (1998) RNA recognition by RNP proteins during RNA processing. Annu. Rev. Biophys. Biomol. Struct. 27:407-445.

Westhof E., Masquida B., Jaeger L. (1996) RNA tectonics : towards RNA design. Folding & Design 1:R78-R88.

Westhof E., Michel F. (1998) Ribozyme architectural diversity made visible. Science 282:251-252.

Wuchty S., Fontana W., Hofacker I. L., Schuster P. (1999) Complete Suboptimal Folding of RNA and the Stability of Secondary Structures. Biopolymers 49:145-165.

Xia T., SantaLucia J. Jr., Burkard M. E., Kierzek R., Schroeder S. J., Jiao X., Cox C., Turner D. H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37:14719-14735 .



Most of the papers co-authored by I. L. Hofacker may be retrieved from this
web address.

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