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An atomistic statistically effective energy function for computational protein Design

Christopher Topham , Sophie Barbe , Isabelle André
Journal of Chemical Theory and Computation, 2016, 12 (8), pp.4146-4168. ⟨10.1021/acs.jctc.6b00090⟩
Journal articles hal-01886411v1
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Structural Investigation of the Thermostability and Product Specificity of Amylosucrase from the Bacterium Deinococcus geothermalis

Frédéric Guerin , Sophie Barbe , Sandra Serin , Gabrielle Veronese , David Guieysse , et al.
Journal of Biological Chemistry, 2012, 287 (9), pp.6642 - 6654. ⟨10.1074/jbc.M111.322917⟩
Journal articles hal-01268407v1

Mechanism of HIV-1 integrase inhibition by styrylquinoline derivatives in vitro.

Eric Deprez , Sophie Barbe , Macieij Kolaski , Hervé Leh , Fatima Zouhiri , et al.
Molecular Pharmacology, 2004, 65 (1), pp.85-98. ⟨10.1124/mol.65.1.85⟩
Journal articles hal-00247990v1
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Modulation de l'interaction intégrase/ADN du VIH-1 par des dérivés des styrylquinoléines et par la modification de nucléotides

Sophie Barbe
Biochimie [q-bio.BM]. École normale supérieure de Cachan - ENS Cachan, 2006. Français. ⟨NNT : ⟩
Theses tel-00129455v1
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The covalent complex of Jo-In results from a long-lived, non-covalent intermediate state with near-native structure

Neil Cox , Cyril Charlier , Ramadoss Vijayaraj , Marion de La Mare , Sophie Barbe , et al.
Biochemical and Biophysical Research Communications, 2021, 589, pp.223-228. ⟨10.1016/j.bbrc.2021.12.028⟩
Journal articles hal-03554277v1
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Guaranteed Weighted Counting for Affinity Computation: Beyond Determinism and Structure

Clement Viricel , David Simoncini , Sophie Barbe , Thomas Schiex
CP16 - 22nd International Conference on the Principles and Practice of Constraint Programming, Sep 2016, Toulouse, France. pp.18, ⟨10.1007/978-3-319-44953-1_46⟩
Conference papers hal-01828389v1

Guaranteed Diversity & Quality for the Weighted CSP

Manon Ruffini , Jelena Vucinic , Simon de Givry , George Katsirelos , Sophie Barbe , et al.
2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI), Nov 2019, Portland, United States. pp.18-25, ⟨10.1109/ICTAI.2019.00012⟩
Conference papers hal-03181764v1

Computational strategy for protein design based on structure-dynamics-activity relationship insights: GH11Xylanases as a casestudy

Gleb Novikov , Jelena Vucinic , Cedric Montanier , Thomas Schiex , Claire Dumon , et al.
13. Carbohydrate Bioengineering Meeting, May 2019, Toulouse, France
Poster communications hal-02928929v1
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Structural Investigation of the Thermostability and Product Specificity of Amylosucrase from the BacteriumDeinococcus geothermalis

Frédéric Guerin , Sophie Barbe , Sandra Pizzut-Serin , Gabrielle Potocki-Veronese , David Guieysse , et al.
Journal of Biological Chemistry, 2011, 287, pp.6642 - 6654. ⟨10.1074/jbc.m111.322917⟩
Journal articles hal-03003044v1
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Cost Function Networks to Solve Large Computational Protein Design Problems

David Allouche , Sophie Barbe , Simon de Givry , George Katsirelos , Yahia Lebbah , et al.
Malek Masmoudi, Bassem Jarboui, Patrick Siarry. Operations Research and Simulation in healthcare, Springer, pp.81-102, 2021, 978-3-030-45223-0. ⟨10.1007/978-3-030-45223-0_4⟩
Book sections hal-02177634v1

Mutant yeast strain capable of producing medium chain fatty acids

Florence Bordes , C. Rigouin , Alain Marty , Marc Guéroult , Isabelle Andre , et al.
France, Patent n° : EP17305044. 2016
Patents hal-02963117v1

CAZyme discovery and design for sweet dreams

Isabelle André , Gabrielle Veronese , Sophie Barbe , Claire Moulis , Magali Remaud Simeon
Current Opinion in Chemical Biology, 2014, 19, pp.17-24. ⟨10.1016/j.cbpa.2013.11.014⟩
Journal articles hal-01268759v1
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An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase MtLYR3

Younes Bouchiba , Jérémy Esque , Ludovic Cottret , Maude Maréchaux , Mégane Gaston , et al.
Protein Science, 2022, 31 (6), 17 p. ⟨10.1002/pro.4327⟩
Journal articles hal-03684572v1
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Computer-aided engineering of a branching sucrase for the glucodiversification of a tetrasaccharide precursor of S. flexneri antigenic oligosaccharides

Mounir Benkoulouche , Akli Ben Imeddourene , Louis-Antoine Barel , Dorian Lefebvre , Mathieu Fanuel , et al.
Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-99384-9⟩
Journal articles hal-03382404v1
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Fitness Landscape Analysis around the Optimum in Computational Protein Design

David Simoncini , Sophie Barbe , Thomas Schiex , Sébastien Verel
Genetic and Evolutionary Computation Conference (GECCO) 2018, Jul 2018, Kyoto, Japan
Conference papers hal-01823638v1
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Constraint Programming and Graphical models - Pushing data into your models, The protein design case.

Thomas Schiex , Sophie Barbe , David Simoncini , Jelena Vucinic , Manon Ruffini , et al.
23rd International Symposium on Mathematical Programming (ISMP-18), Jul 2018, Bordeaux, France
Conference papers hal-02154354v1
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A tripartite carbohydrate-binding module to functionalize cellulose nanocrystal

Angeline Pelus , Gaëlle Bordes , Sophie Barbe , Younes Bouchiba , Callum Burnard , et al.
Biomaterials Science, 2021, 9 (22), pp.7444-7455. ⟨10.1039/d1bm01156a⟩
Journal articles hal-03372120v1

Effect of a water molecule on the sugar puckering of uridine, 2'-deoxyuridine, and 2'-O-methyl uridine inserted in duplexes.

Sophie Barbe , Marc Le Bret
Journal of Physical Chemistry A, 2008, 112 (5), pp.989-99. ⟨10.1021/jp075777u⟩
Journal articles istex hal-00359088v1
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Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems

Antoine Charpentier , David Mignon , Sophie Barbe , Juan Cortés , Thomas Schiex , et al.
Journal of Chemical Information and Modeling, 2019, 59 (1), pp.127-136. ⟨10.1021/acs.jcim.8b00510⟩
Journal articles hal-01943616v1
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Approximate counting with deterministic guarantees for affinity computation

Clément Viricel , David Simoncini , David Allouche , Simon de Givry , Sophie Barbe , et al.
3. International Conference on Modelling, Computation and Optimization in Information Systems and Management Sciences - MCO 2015, Université de Lorraine (UL). FRA., May 2015, Metz, France. 500 p., ⟨10.1007/978-3-319-18167-7_15⟩
Conference papers hal-01269259v1


Christopher Topham , Hélène Texier , Vincent Tournier , Marie-Laure Desrousseaux , Sophie Duquesne , et al.
France, Patent n° : WO/2018/011284. 2018
Patents hal-02961834v1
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Molecular flexibility in computational protein design: an algorithmic perspective

Younes Bouchiba , Juan Cortés , Thomas Schiex , Sophie Barbe
Protein Engineering, Design and Selection, 2021, 34, pp.gzab011. ⟨10.1093/protein/gzab011⟩
Journal articles hal-03221838v1

Engineering of anp efficient mutant of Neisseria polysaccharea amylosucrase for the synthesis of controlled size maltooligosaccharides

Alizée Verges , Sophie Barbe , Emmanuelle Cambon , Claire Moulis , Samuel Tranier , et al.
Carbohydrate Polymers, 2017, 173, pp.403-411. ⟨10.1016/j.carbpol.2017.06.011⟩
Journal articles hal-01602744v1

Production of medium chain fatty acids by Yarrowia lipolytica: Combining molecular design and TALEN to engineer the fatty acid synthase

Coraline Rigouin , Marc Gueroult , Christian Croux , Gwendoline Dubois , Vinciane Borsenberger , et al.
ACS Synthetic Biology, 2017, ⟨10.1021/acssynbio.7b00034⟩
Journal articles hal-01605956v1
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Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase

Sota Yagi , Aditya K Padhi , Jelena Vucinic , Sophie Barbe , Thomas Schiex , et al.
Journal of the American Chemical Society, In press, 143 (39), pp.15998-16006. ⟨10.1021/jacs.1c05367⟩
Journal articles hal-03360584v1
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Enzyme Active Site Loop Revealed as a Gatekeeper for Cofactor Flip by Targeted Molecular Dynamics Simulations and FRET-Based Kinetics

Sophie Rahuel-Clermont , Raphaël Bchini , Sophie Barbe , Séverine Boutserin , Isabelle André , et al.
ACS Catalysis, 2019, 9 (2), pp.1337-1346. ⟨10.1021/acscatal.8b03951⟩
Journal articles hal-02022828v1

Insights into lid movements of Burkholderia cepacia lipase inferred from molecular dynamics simulations

Sophie Barbe , Vincent Lafaquière , David Guieysse , Pierre Monsan , Magali Remaud Simeon , et al.
Proteins - Structure, Function and Bioinformatics, 2009, 77 (3), pp.509-523. ⟨10.1002/prot.22462⟩
Journal articles hal-02660544v1

Guaranteed Discrete Energy Optimization on Large Protein Design Problems

David Simoncini , David Allouche , Simon de Givry , Céline Delmas , Sophie Barbe , et al.
Journal of Chemical Theory and Computation, 2015, 11 (12), pp.5980 - 5989. ⟨10.1021/acs.jctc.5b00594⟩
Journal articles hal-02637306v1

Computational protein design as a cost function network optimization problem

Thomas Schiex , David Allouche , Simon de Givry , George Katsirelos , Sophie Barbe , et al.
Séminaire MOGISA du LAAS/CNRS, Centre National de la Recherche Scientifique (CNRS). FRA., Jun 2013, Toulouse, France
Conference papers hal-01268632v1
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Three ParA Dimers Cooperatively Assemble on Type Ia Partition Promoters

François Boudsocq , Maya Salhi , Sophie Barbe , Jean-Yves Bouet
Genes, 2021, 12 (9), ⟨10.3390/genes12091345⟩
Journal articles hal-03358090v1