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Fabrice Leclerc

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39
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Presentation

![](https://www.i2bc.paris-saclay.fr/wp-content/uploads/2021/04/Artistic-view-of-a-possible-RNA-world-1024x490.png) CNRS senior scientist (Ph.D. Biochemistry) in the field of RNA bioinformatics at the University Paris Saclay. I develop and apply modeling approaches to understand the structure/function relationships of RNAs (sequence, 2D, and 3D structure). My research interests include RNomics (identification and characterization of non-coding RNA genes), computational enzymology (elucidate the catalysis by self-cleaving ribozymes), docking (model and predict RNA/protein interactions), and fragment-based design of oligonucleotides. [https://www.i2bc.paris-saclay.fr/equipe-rna-sequence-structure-function/](https://www.i2bc.paris-saclay.fr/equipe-rna-sequence-structure-function/ "RNA Sequence, Structure & Function")

Publications

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BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics

Roy González-Alemán , Daniel Platero-Rochart , David Hernández-Castillo , Erix Hernández-Rodríguez , Julio Caballero
Bioinformatics, 2022, 38 (1), pp.73-79. ⟨10.1093/bioinformatics/btab595⟩
Journal articles hal-03767725v1
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MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics

Roy González-Alemán , Daniel Platero-Rochart , Alejandro Rodríguez-Serradet , Erix Hernández-Rodríguez , Julio Caballero
Bioinformatics, 2022, 38 (23), pp.5191-5198. ⟨10.1093/bioinformatics/btac666⟩
Journal articles hal-03938219v1
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Prediction of molecular interactions and physicochemical properties relevant for vasopressin V2 receptor antagonism

Ania de la Nuez Veulens , Yoanna Ginarte , Rolando Fernandez , Fabrice Leclerc , Luis Cabrera
Journal of Molecular Modeling, 2022, 28 (2), pp.31. ⟨10.1007/s00894-021-05022-6⟩
Journal articles hal-03767713v1
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RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics

Daniel Platero-Rochart , Roy González-Alemán , Erix Hernández-Rodríguez , Fabrice Leclerc , Julio Caballero
Bioinformatics, 2022, 38 (7), pp.1863-1869. ⟨10.1093/bioinformatics/btac021⟩
Journal articles hal-03767732v1
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MCSS-based Predictions of Binding Mode and Selectivity of Nucleotide Ligands

Roy González-Alemán , Nicolas Chevrollier , Manuel Simoes , Luis Montero-Cabrera , Fabrice Leclerc
Journal of Chemical Theory and Computation, 2021, ⟨10.1021/acs.jctc.0c01339⟩
Journal articles hal-03174156v1
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MCSS-based Predictions of Binding Mode and Selectivity of Nucleotide Ligands

Roy Gonzalez-Aleman , Nicolas Chevrollier , Manuel Simoes , Luis Montero-Cabrera , Fabrice Leclerc
Journal of Chemical Theory and Computation, 2021, 17 (4), pp.2599-2618. ⟨10.1021/acs.jctc.0c01339⟩
Journal articles hal-02116374v3
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Ribozyme Chemistry: to be or not to be under high pressure

Marie Christine Maurel , Fabrice Leclerc , Guy Hervé
Chemical Reviews, 2019, 120 (11), pp.4898-4918. ⟨10.1021/acs.chemrev.9b00457⟩
Journal articles hal-02317015v2
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RNA Back and Forth: Looking through Ribozyme and Viroid Motifs

Marie-Christine Maurel , Fabrice Leclerc , Jacques Vergne , Giuseppe Zaccai
Viruses, 2019, 11 (3), pp.283. ⟨10.3390/v11030283⟩
Journal articles hal-02104510v1
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From Foundation Stones to Life: Concepts and Results

Marie-Christine Maurel , Fabrice Leclerc
Elements, 2016, 12 (6), pp.407 - 412. ⟨10.2113/gselements.12.6.407⟩
Journal articles hal-01489685v1
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Self-assembly Controls Self-cleavage of HHR from ASBVd (−): a Combined SANS and Modeling Study

Fabrice Leclerc , Giuseppe Zaccai , Jacques Vergne , Martina Řìhovà , Anne Martel
Scientific Reports, 2016, 6 (30287), ⟨10.1038/srep30287⟩
Journal articles hal-01357443v1
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Revisiting the structure/function relationships of H/ACA(-like) RNAs: A unified model for Euryarchaea and Crenarchaea

Claire Toffano-Nioche , Daniel Gautheret , Fabrice Leclerc
Nucleic Acids Research, 2015, 43 (16), pp.7744-7761. ⟨10.1093/nar/gkv756⟩
Journal articles hal-01464539v1
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RNA at 92 °C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.

Claire Toffano-Nioche , Alban Ott , Estelle Crozat , an N Nguyen , Matthias Zytnicki
RNA Biology, 2013, 10 (7), pp.1211-20. ⟨10.4161/rna.25567⟩
Journal articles hal-00863721v1
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Comparative Study of Two Box H/ACA Ribonucleoprotein Pseudouridine-Synthases

Jean-Baptiste Fourmann , Anne-Sophie Tillault , Magali Blaud , Fabrice Leclerc , Christiane Branlant
PLoS ONE, 2013, 8 (7), pp.e70313. ⟨10.1371/journal.pone.0070313⟩
Journal articles hal-01452159v1
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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali , Cédric Saule , Cedric Chauve , Yves d'Aubenton-Carafa , Alain Denise
Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩
Journal articles hal-00647725v1
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Modeling the RNA 2′OH activation: possible roles of metal ion and nucleobase as catalysts in self-cleaving ribozymes

Zdeněk Chval , Daniela Chvalová , Fabrice Leclerc
Journal of Physical Chemistry B, 2011, 115 (37), pp.10943-10956. ⟨10.1021/jp200970d⟩
Journal articles hal-03992490v1
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Two-Metal-Ion Mechanism for Hammerhead-Ribozyme Catalysis

Fabrice Leclerc , Martin Karplus
Journal of Physical Chemistry B, 2006, 110 (7), pp.3395-3409. ⟨10.1021/jp053835a⟩
Journal articles hal-03992512v1
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Nucleophilic Attack on Phosphate Diesters: A Density Functional Study of In−Line Reactivity in Dianionic, Monoanionic, and Neutral Systems

Xabier Lopez , Annick Dejaegere , Fabrice Leclerc , Darrin M York , Martin Karplus
Journal of Physical Chemistry B, 2006, 110 (23), pp.11525-11539. ⟨10.1021/jp0603942⟩
Journal articles hal-04003725v1
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MCSS-based predictions of RNA binding sites

Fabrice Leclerc , Martin Karplus
Theoretical Chemistry Accounts: Theory, Computation, and Modeling, 1998, 101, pp.131-137. ⟨10.1007/s002140050419⟩
Journal articles hal-03992529v1
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Relating conformation, Mg2+ binding, and functional group modification in the hammerhead ribozyme.

P Chartrand , Fabrice Leclerc , R Cedergren
RNA, 1997, 3 (7), pp.692-6
Journal articles hal-04003668v1
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Using SAR and QSAR analysis to model the activity and structure of the quinolone—DNA complex

Belsis Llorente , Fabrice Leclerc , Robert Cedergren
Bioorganic and Medicinal Chemistry Letters, 1996, 4 (1), pp.61-71. ⟨10.1016/0968-0896(96)83749-7⟩
Journal articles hal-03992555v1
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Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs

Taher Yacoub , Roy González-Alemán , Fabrice Leclerc , Isaure Chauvot de Beauchêne , Yann Ponty
RECOMB 2024 - 28th International Conference of Research in Computational Molecular Biology, Apr 2024, Boston, United States
Conference papers hal-03816423v3
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Identification of selective inhibitors against BACE 1 over BACE 2 in Alzheimer’s disease by Quantitative Structure-Activity Relationship (QSAR)

Yoanna Álvarez Ginarte , Roy González Aleman , Taher Yacoub , Fabrice Leclerc , Luis A. Montero Cabrera
Neuroscience and Neurotechnology in the 21st century Symposium / BioHabana2022, Apr 2022, La Havane, Cuba
Conference papers hal-03669386v1

Design of oligonucleotides as RNA-based drugs: prerequisites and opportunities for in silico methods within the framework of fragment-based approaches

Fabrice Leclerc
Mini-symposium@JOBIM 2020 - RNA structure, design and interactions with proteins, Jul 2020, Montpellier (en ligne), France
Conference papers hal-03313254v1

Modified oligonucleotides as RNA-based drugs (biosensors): prerequisites and opportunities for in silico methods within the framework of fragment-based approaches

Fabrice Leclerc
GDR RNA: 1st Scientific Meeting, Nov 2020, Nice (en ligne), France
Conference papers hal-03313276v1

MCSS with hybrid solvent models: qualitative docking & screening powers of nucleotidic ligands

Fabrice Leclerc
CHARMM Meeting 2020, Jul 2020, Cambridge, MA, United States
Conference papers hal-03313271v1

Integrative Model of Rhodanine Derivatives as Tau- aggregation inhibitors in AD

Fabrice Leclerc , Yoanna Álvarez Ginarte
7th International Chemistry Symposium SIQ - SEADIM / 12th Molecular Design and Bioinformatics Symposium, Jun 2019, Cayo Santa María, Cuba
Conference papers hal-02324217v1

MCSS Update biomolecular fragments solvent models, scoring functions, … and application examples to oligonucleotides

Fabrice Leclerc
Charmm-Tinker meeting (2019), Jul 2019, Paris, France
Conference papers hal-02324203v1

Benchmarking RNA secondary structure comparison algorithms

Julien Allali , Yves d'Aubenton-Carafa , Cedric Chauve , Alain Denise , Christine Drevet
JOBIM'08, 2008, Lille, France. pp.67-68
Conference papers hal-00375710v1

Analyse des Séquences InterORF chez les Levures - Application à la Recherche des petits ARN

Emmanuel Gothié , Yann Guermeur , Fabrice Leclerc , Christiane Branlant , Alexander Bockmayr
Structure, Intégration, Fonction et Réactivité des ARN - SIFRARN, Oct 2002, Nancy, France
Conference papers inria-00101006v1
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Drawing and Editing the Secondary Structure(s) of RNA.

Yann Ponty , Fabrice Leclerc
Ernesto Picardi. RNA Bioinformatics, 1269, Springer New York, pp.63-100, 2015, Methods in Molecular Biology, 978-1-4939-2290-1. ⟨10.1007/978-1-4939-2291-8_5⟩
Book sections hal-01079893v1
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Contributions des approches moléculaires $in\ silico$ à la compréhension des liens structure/fonction des ARN

Fabrice Leclerc
Biophysique. Université Henri Poincaré (Nancy 1), 2009
Habilitation à diriger des recherches tel-03987025v1
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Contributions des approches moléculaires in silico à la compréhension des liens structure/fonction des ARN

Fabrice Leclerc
Bio-informatique [q-bio.QM]. Université Henri Poincaré – Nancy I, 2009
Habilitation à diriger des recherches tel-03607902v1