Eric Westhof

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Milestones in Molecular Dynamics Simulations of RNA Systems

Yaser Hashem, Eric Westhof, Pascal Auffinger, 2008 .

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

Eric Westhof, Zhichao Miao, Zhichao Miao, 2015, PLoS Comput. Biol..

Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

Eric Westhof, Steinar D Johansen, Henrik Nielsen, 2008, The EMBO journal.

BIOINFORMATICS APPLICATIONS NOTE

Eric Westhof, Fabrice Jossinet, Thomas E. Ludwig, 2022 .

Fidelity of translation: structural view

Eric Westhof, A. Rozov, Natalia Demeshkina, 2015 .

RNA Structure: Advances and Assessment of 3D Structure Prediction.

Eric Westhof, Zhichao Miao, Zhichao Miao, 2017, Annual review of biophysics.

Tools for the automatic identification and classification of RNA base pairs

John D. Westbrook, Helen M. Berman, Huanwang Yang, 2003, Nucleic Acids Res..

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure

Eric Westhof, Fabrice Jossinet, E. Westhof, 2005, Bioinform..

Advances in RNA 3D Structure Modeling Using Experimental Data

Eric Westhof, Yang Cao, Zhichao Miao, 2020, Frontiers in Genetics.

Solution structure of human U1 snRNA. Derivation of a possible three- dimensional model

Eric Westhof, M. Bach, J. P. Ebel, 1990, Nucleic Acids Res..

Faculty Opinions recommendation of Biological networks.

Eric Westhof, 2003 .

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database

Eric Westhof, Zhichao Miao, Zhichao Miao, 2016, Nucleic Acids Res..

Automated prediction of three-way junction topological families in RNA secondary structures

Dominique Barth, Alain Denise, Franck Quessette, 2012, Comput. Biol. Chem..

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Karen Eilbeck, Michel Dumontier, Robert Hoehndorf, 2009, Appl. Ontology.

Modeling the Architecture of Structured RNAs within a Modular and Hierarchical Framework

Eric Westhof, Benoît Masquida, E. Westhof, 2008 .

Searching genomes for ribozymes and riboswitches

Eric Westhof, E. Westhof, C. Hammann, 2007, Genome Biology.

Simulations of the dynamics at an RNA–protein interface

Thomas Hermann, Eric Westhof, E. Westhof, 1999, Nature Structural Biology.

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families

Alain Denise, Jérôme Waldispühl, Vladimir Reinharz, 2018, Nucleic acids research.

Evolution of RNA Architecture

Eric Westhof, E. Westhof, C. Massire, 2004, Science.

23 A Modular and Hierarchical Approach for All-Atom RNA Modeling

Eric Westhof, Benoît Masquida, 2006 .

Distinctive structures between chimpanzee and human in a brain noncoding RNA.

Eric Westhof, E. Westhof, A. Krol, 2008, RNA.

Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI

Eric Westhof, Alexis Autour, Michael Ryckelynck, 2017, RNA.

Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding.

Tao Pan, Eric Westhof, Tobin R Sosnick, 2005, Journal of molecular biology.

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.

Feng Ding, Kristian Rother, Thomas Hermann, 2012, RNA.

Base pairing constraints drive structural epistasis in ribosomal RNA sequences.

Eric Westhof, Fabrice Jossinet, E. Westhof, 2010, Molecular biology and evolution.

New metrics for comparing and assessing discrepancies between RNA 3D structures and models.

Eric Westhof, François Major, Marc Parisien, 2009, RNA.

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

Eric Westhof, Pascal Auffinger, E. Westhof, 2002, Biophysical chemistry.

Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations.

Eric Westhof, Pascal Auffinger, Lukasz Bielecki, 2004, Journal of molecular biology.

Comparative genomics of protoploid Saccharomycetaceae.

Adrien Goëffon, Macha Nikolski, Pascal Durrens, 2009, Genome research.

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution

Johannes Söding, Michael Habeck, Eric Westhof, 2010, Proceedings of the National Academy of Sciences.

Single Processing Center Models for Human Dicer and Bacterial RNase III

Eric Westhof, E. Westhof, W. Filipowicz, 2004, Cell.

Pronounced instability of tandem IU base pairs in RNA.

Eric Westhof, E. Westhof, M. Serra, 2004, Nucleic acids research.

The RNA Ontology Consortium: an open invitation to the RNA community.

James W. Brown, Helen M Berman, Steven E Brenner, 2006, RNA.

The amazing world of bacterial structured RNAs

Eric Westhof, E. Westhof, 2010, Genome Biology.

Twenty years of RNA crystallography.

Eric Westhof, 2015, RNA.

MULTIPLE MOLECULAR DYNAMICS SIMULATIONS OF THE ANTICODON LOOP OF TRNAASP IN AQUEOUS SOLUTION WITH COUNTERIONS

Eric Westhof, Pascal Auffinger, E. Westhof, 1995 .

RNA as a Drug Target: The Case of Aminoglycosides

Eric Westhof, Quentin Vicens, E. Westhof, 2003, Chembiochem : a European journal of chemical biology.

RNA 3D Structure Analysis and Prediction

Eric Westhof, Neocles B. Leontis, E. Westhof, 2012, Nucleic Acids and Molecular Biology.

Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome

Klaus Schulten, Eric Westhof, Shashi Bhushan, 2009, Science.

The Molecular Basis for A‐Site Mutations Conferring Aminoglycoside Resistance: Relationship between Ribosomal Susceptibility and X‐ray Crystal Structures

Eric Westhof, Quentin Vicens, E. Westhof, 2003, Chembiochem : a European journal of chemical biology.

The Dynamic Landscapes of RNA Architecture

Eric Westhof, José Almeida Cruz, E. Westhof, 2009, Cell.

Halogen bonds in biological molecules.

Eric Westhof, Pascal Auffinger, P Shing Ho, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Eric Westhof, Benoît Masquida, E. Westhof, 2003, Proceedings of the National Academy of Sciences of the United States of America.

MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences

Patrice Koehl, Olivier Poch, Stephen R. Holbrook, 2005, Nucleic acids research.

Predicting and modeling RNA architecture.

Eric Westhof, Fabrice Jossinet, Benoît Masquida, 2011, Cold Spring Harbor perspectives in biology.

Molecular Dynamics: Simulations of Nucleic Acids

Eric Westhof, Pascal Auffinger, E. Westhof, 2002 .

Docking of aminoglycosides to hydrated and flexible RNA.

Stephen Hanessian, Nicolas Moitessier, Eric Westhof, 2006, Journal of medicinal chemistry.

The Architectural Motifs of Folded RNAs

Eric Westhof, E. Westhof, V. Fritsch, 2010 .

Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding

Eric Westhof, Quentin Vicens, Benoît Masquida, 2005, Nucleic acids research.

Sequence-based identification of 3D structural modules in RNA with RMDetect

Eric Westhof, José Almeida Cruz, E. Westhof, 2011, Nature Methods.

An mRNA Is Capped by a 2', 5' Lariat Catalyzed by a Group I-Like Ribozyme

Eric Westhof, Henrik Nielsen, Steinar Johansen, 2005, Science.

Recurrent RNA Motifs

Eric Westhof, Neocles B. Leontis, 1999 .

Structural insights into the translational infidelity mechanism

Eric Westhof, E. Westhof, M. Yusupov, 2015, Nature Communications.

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

Janusz M Bujnicki, Tomasz Zok, Jakub Wiedemann, 2019, Nucleic acids research.

The RNA structurome: high-throughput probing

Eric Westhof, Pascale Romby, E. Westhof, 2010, Nature Methods.

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Feng Ding, Jian Wang, Janusz M Bujnicki, 2015, RNA.

Water and Biological Macromolecules

Eric Westhof, E. Westhof, 1993 .

Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions

Andrew D Griffiths, Eric Westhof, Michael Ryckelynck, 2015, RNA.

Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments

Eric Westhof, Neocles B. Leontis, E. Westhof, 2005, Nucleic acids research.

Frequency and isostericity of RNA base pairs

Eric Westhof, Jesse Stombaugh, Craig L. Zirbel, 2009, Nucleic acids research.

Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide.

Eric Westhof, Quentin Vicens, E. Westhof, 2003, Journal of molecular biology.

Metal ion binding to RNA.

Eric Westhof, Pascal Auffinger, Neena Grover, 2011, Metal ions in life sciences.

Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate

Frédéric Delsuc, Boris Lenhard, Hans Lehrach, 2010, Science.

Structural biology. Evolution of RNA architecture.

Eric Westhof, Christian Massire, 2004, Science.

The non-Watson-Crick base pairs and their associated isostericity matrices.

Eric Westhof, Jesse Stombaugh, Neocles B Leontis, 2002, Nucleic acids research.

RNA pseudoknots

Luc Jaeger, Eric Westhof, E. Westhof, 1992, Current Biology.

Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme.

Eric Westhof, Venkat Gopalan, Benoît Masquida, 2003, Journal of molecular biology.

Functional Hammerhead Ribozymes Naturally Encoded in the Genome of Arabidopsis thalianaw⃞

Eric Westhof, Gerhard Steger, Stefan Gräf, 2005, The Plant Cell Online.

RNA Tertiary Structure

Eric Westhof, Pascal Auffinger, E. Westhof, 2006 .

Structure of the ribosome-bound cricket paralysis virus IRES RNA

Eric Westhof, E. Westhof, P. Penczek, 2006, Nature Structural &Molecular Biology.

Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes.

Christoph Flamm, Eric Westhof, C. Flamm, 2004, Nucleic acids research.

Toward atomic accuracy in RNA design

Eric Westhof, E. Westhof, 2010, Nature Methods.

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Feng Ding, Janusz M Bujnicki, Lin Huang, 2020, RNA.

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures.

Eric Westhof, E. Westhof, M. Serra, 2002, RNA.