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Structure: Internal structure identifier : 489

Coopérative effects in the photophysical properties of DNA oligomers

D. Markovitsi , B. Bouvier , J.-P. Dognon , T. Gustavsson , R. Lavery , et al.
XX IUPAC Symposium on Photochemistry, 2004, Grenade, Spain
Conference papers hal-00087784v1
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Holding the Nucleosome Together: A Quantitative Description of the DNA–Histone Interface in Solution

Ahmad Elbahnsi , Romain Retureau , Marc Baaden , Brigitte Hartmann , Christophe Oguey
Journal of Chemical Theory and Computation, 2018, 14 (2), pp.1045 - 1058. ⟨10.1021/acs.jctc.7b00936⟩
Journal articles hal-01935581v1
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Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data

Mikael Trellet , Nicolas Ferey , Jakub Flotyński , Marc Baaden , Patrick Bourdot
Journal of Integrative Bioinformatics, 2018, 15 (2), pp.20180004. ⟨10.1515/jib-2018-0004⟩
Journal articles hal-01935586v1
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Navigation guidée par le contenu pour l'exploration moléculaire.

M. Trellet , N. Férey , M. Baaden , P. Bourdot
Journées de l’Association Française de Réalité Virtuelle (AFRV), 2013, Laval, France
Conference papers hal-01498083v1
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The interplay between molecular flexibility and RNA chemical probing reactivities analyzed at the nucleotide level via an extensive molecular dynamics study

Elisa Frezza , Antoine Courban , Delphine M Allouche , Bruno Sargueil , Samuela Pasquali
Methods, 2019, 162-163, pp.108-127. ⟨10.1016/j.ymeth.2019.05.021⟩
Journal articles hal-02387476v1

Applications to water transport systems: general discussion

Marc Baaden , Mihail Barboiu , Manash Pratim Borthakur , Chun-Long Chen , Rob Coalson , et al.
Faraday Discussions, 2018, 209, pp.389 - 414. ⟨10.1039/C8FD90022A⟩
Journal articles hal-01926896v1
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Ten simple rules to create a serious game, illustrated with examples from structural biology

Marc Baaden , Olivier Delalande , Nicolas Ferey , Samuela Pasquali , Jérôme Waldispühl , et al.
PLoS Computational Biology, 2018, 14 (3), pp.e1005955. ⟨10.1371/journal.pcbi.1005955⟩
Journal articles hal-01744190v1

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

Alex Tek , Benoist Laurent , Marc Piuzzi , Zhihan Lu , Matthieu Chavent , et al.
Weibo Cai and Hao Hong. Biochemistry, Genetics and Molecular Biology " "Protein-Protein Interactions - Computational and Experimental Tools", InTech, pp.27-65, 2012, 978-953-51-0397-4. ⟨10.5772/36568⟩
Book sections hal-00760181v1

Amyloid beta Protein and Alzheimer\textquoterights Disease: When Computer Simulations Complement Experimental Studies

Jessica Nasica-Labouze , Phuong H. Nguyen , Fabio Sterpone , Olivia Berthoumieu , Nicolae-Viorel Buchete , et al.
Chem. Rev., 2015, 115 (9), pp.3518--3563. ⟨10.1021/cr500638n⟩
Journal articles hal-01498025v1

Changes in protein structure at the interface accompanying complex formation.

Devlina Chakravarty , Joel Janin , Charles H. Robert , Pinak Chakrabarti
International Union of Crystallography journal, 2015, 2 (Pt 6), pp.643--652. ⟨10.1107/S2052252515015250⟩
Journal articles hal-01498035v1

Molecular Mechanism of the Cell Membrane Pore Formation Induced by Bubble Stable Cavitation

Viet Hoang Man , Phan Minh Truong , Mai Suan Li , Junmei Wang , Nguyen-Thi Van-Oanh , et al.
Journal of Physical Chemistry B, 2018, 123 (1), pp.71-78. ⟨10.1021/acs.jpcb.8b09391⟩
Journal articles hal-02381311v1

Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses

Viet Hoang Man , Nguyen-Thi Van-Oanh , Philippe Derreumaux , Mai Suan Li , Christopher Roland , et al.
Physical Chemistry Chemical Physics, 2016, 18 (17), pp.11951--11958. ⟨10.1039/c5cp07711g⟩
Journal articles hal-01497987v1
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BioSpring: an interactive and multi-resolution software for flexible docking and for mechanical exploration of large biomolecular assemblies

Nicolas Ferey , Olivier Delalande , Marc Baaden
JOBIM 2012 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp.433-434
Conference papers hal-00761683v1

Absorption spectra and photochemistry of DNA oligomers

E. Emanuele , R. Lavery , Sylvie Marguet , D. Markovitsi , P. Millie , et al.
Pacifichem 2005 : Phtophysical Dynamics in Biological Molecules), 2005, Honolulu, Hawai, United States
Conference papers hal-00088177v1

Non-equivalent binding sites for Abeta1-40 on PrP determine the oligomerisation pathway

Katarina Grznarova , Joan Torrent , Carola Munoz Montesino , Jessica Nasica , Philippe Derreumaux , et al.
Non equivalent binding sites for Abeta1-40 on PrP determine the oligomerisation pathway, 2016, PHILADELPHIA, United States. pp.1
Conference papers hal-02740033v1
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Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening

Paulo R Batista , Gaurav Pandey , Pedro G Pascutti , Paulo M Bisch , David Perahia , et al.
Journal of Chemical Theory and Computation, 2011, 7 (8), pp.2348-2352. ⟨10.1021/ct200237u⟩
Journal articles hal-02988887v1
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Itinéraires Bis

Axel Kahn , Sebastien Fleuret , Sébastien Descotes-Genon , Nicolas B. Garnier , Carole Levenes , et al.
2009, Connaissance et savoirs, 978-2-7539-0164-3
Books halshs-02424173v1
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ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations

Matthieu Dreher , Jessica Prevoteau-Jonquet , Mikael Trellet , Marc Piuzzi , Marc Baaden , et al.
Faraday Discussions, 2014, Molecular simulations and visualization, 169, pp.119-142. ⟨10.1039/C3FD00142C⟩
Journal articles hal-00942627v1

Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes

Petr Stadlbauer , Liuba Mazzanti , Tristan Cragnolini , David J. Wales , Philippe Derreumaux , et al.
Journal of Chemical Theory and Computation, 2016, 12 (12), pp.6077--6097. ⟨10.1021/acs.jctc.6b00667⟩
Journal articles hal-01497979v1

Water Determines the Structure and Dynamics of Proteins

M-C. Bellissent-Funel , A. Hassanali , M. Havenith , R. Henchman , P. Pohl , et al.
Chemical Reviews, 2016, 116 (13), pp.7673-7697. ⟨10.1021/acs.chemrev.5b00664⟩
Journal articles hal-01498000v1

What Computational Methods can Teach us about the Alzheimer-Protective Nature of A2V-and A2T-Mutant Amyloid-Beta Oligomers

Jessica Nasica-Labouze , Bogdan Tarus , Phuong Nguyen , Philippe Derreumaux
Biophys. J., 2015, Unknown, Unknown Region. pp.204A-204A
Conference papers hal-01498022v1

Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp

Olivia Berthoumieu , Phuong H. Nguyen , Maria P. Del Castillo-Frias , Sabrina Ferre , Bogdan Tarus , et al.
Chemistry - A European Journal, 2015, 21 (36), pp.12657--12666. ⟨10.1002/chem.201500888⟩
Journal articles istex hal-01498029v1

Reassessing buried surface areas in protein-protein complexes.

Devlina Chakravarty , Mainak Guharoy , Charles H. Robert , Pinak Chakrabarti , Joel Janin
Protein Sci., 2013, 22, pp.1453--57. ⟨10.1002/pro.2330⟩
Journal articles hal-01498068v1
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Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions

Olivier Delalande , Anne-Elisabeth Molza , Raphael dos Santos Morais , Angélique Chéron , Emeline Pollet , et al.
Journal of Biological Chemistry, 2018, 293 (18), pp.6637-6646. ⟨10.1074/jbc.M117.809798⟩
Journal articles hal-01795395v2

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.

Sarel J Fleishman , Timothy A Whitehead , Eva-Maria Strauch , Jacob E Corn , Sanbo Qin , et al.
Journal of Molecular Biology, 2011, 414 (2), in press. ⟨10.1016/j.jmb.2011.09.031⟩
Journal articles inria-00637848v1
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Exciton States of Dynamic DNA Double Helices: Alternating dCdG Sequences

E. Emanuele , K. Zakrzewska , D. Markovitsi , R. Lavery , P. Millie
Journal of Physical Chemistry B, 2005, 109, pp.16109 -16118. ⟨10.1021/jp051833k⟩
Journal articles hal-00084437v1

Exciton states in DNA

D. Markovitsi , E. Emanuele , R. Lavery , P. Millie , K. Zakrzewska
XXII International conference of Photochemistry, 2005, Cairns, Australia
Conference papers hal-00088169v1

Structure of ring-shaped Aβ42 oligomers determined by conformational selection

Linh Tran , Nathalie Basdevant , C Prévost , Tâp Ha-Duong
Scientific Reports, 2016, 6, pp.21429. ⟨10.1038/srep21429⟩
Journal articles hal-01497983v1

Chapter 6: Receptor Flexibility in Ligand Docking and Virtual Screening.

Maria A. Miteva , Charles H. Robert , J. D. Marechal , David Perahia
In-silico lead discovery, Bentham Science Publishers, 2011
Book sections hal-01498123v1

Influence of conformational dynamics on the exciton states of DNA oligomers

B. Bouvier , J.P. Dognon , R. Lavery , D. Markovitsi , P. Millié , et al.
Journal of Physical Chemistry B, 2003, 107, pp.13512-13522. ⟨10.1021/jp036164u⟩
Journal articles istex hal-00094533v1