Publications

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Y
Matte-Tailliez O., Hérisson J., Férey N, Magneau O., Gros P.-E., Képès F., Gherbi R..  2006.  Yeast Naked DNA Spatial Organization Predisposes to Transcriptional Regulation. International Conference on Computational Science and its Applications (ICCSA 2006). 3984:222–231.
Matte-Tailliez O., Hérisson J., Férey N, Magneau O., Gros P.-E., Képès F., Gherbi R..  2006.  Yeast Naked DNA Spatial Organization Predisposes to Transcriptional Regulation. International Conference on Computational Science and its Applications (ICCSA 2006). 3984:222–231.
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Mazur AK.  2007.  Wormlike chain theory and bending of short DNA. Phys. Rev. Lett.. 98:218102.
Mondal J, Stirnemann G, Berne BJ.  2013.  When Does Trimethylamine N-Oxide Fold a Polymer Chain and Urea Unfold It? J. Phys. Chem. B. 117:8723–8732.
Mazzanti L, Doutreligne S, Gageat C, Derreumaux P, Taly A, Baaden M, Pasquali S.  2017.  What Can Human-Guided Simulations Bring to RNA Folding? Biophys J. 113(2):302-312.
Mazur AK.  2017.  Weak nanoscale chaos and anomalous relaxation in DNA. Phys. Rev. E. 95:062417.
Marchi M, Sterpone F, Ceccarelli M.  2002.  Water rotational relaxation and diffusion in hydrated lysozyme. J. Am. Chem. Soc.. 124:6787–91.
Murail S, Vasiliu T, Neamtu A, Barboiu M, Sterpone F, Baaden M.  2018.  Water permeation across artificial I-quartet membrane channels: from structure to disorder.. Faraday Discuss. 209:125-148.
Brovchenko I, Krukau A, Oleinikova A, Mazur AK.  2006.  Water percolation governs polymorphic transitions and conductivity of DNA. Phys. Rev. Lett.. 97:137801.
Brovchenko I, Krukau A, Oleinikova A, Mazur AK.  2007.  Water clustering and percolation in low hydration DNA shells. J. Phys. Chem. B. 111:3258–3266.
Sterpone F, Bertonati C, Briganti G, Melchionna S.  2010.  Water around thermophilic proteins: the role of charged and apolar atoms. J Phys: Cond Matt. 22:284113.
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Garnier C, Briki F, Nedelec B, Le Pogamp P, Dogan A, Rioux-Leclercq N, Goude R, Beugnet C, Martin L, Delpech M et al..  2017.  VLITL is a major cross-β-sheet signal for fibrinogen Aα-chain frameshift variants.. Blood. 130(25):2799-2807.
Valleix S., Derreumaux P, Garnier C., Briki F., Boimard M., Doucet J., Rioux-Leclercq N., Martin L., Grateau G., Delpech M. et al..  2010.  The VLITL aggregation-prone motif might trigger amyloid fibril formation of fibrinogen A alpha-chain frameshift variants in vivo. Amyloid-journal of Protein Folding Disorders. 17:96–97.
Martinez X, Chavent M, Baaden M.  2020.  Visualizing protein structures - tools and trends.. Biochem Soc Trans.
Laureanti J, Brandi J, Offor E, Engel D, Rallo R, Ginovska B, Martinez X, Baaden M, Baker NA.  2020.  Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS.. Protein Sci. 29(1):237-246.
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Férey N, Bouyer G., Martin C., Bourdot P., Nelson J., Burkhardt andJM.  2008.  User Needs Analysis to Design a 3D Multimodal Protein-Docking Interface. Symposium on 3D User Interfaces 2008 (3DUI 2008 - IEEE). :125–132.
Timsit Y, Westhof E., Fuchs R.P., Moras D..  1989.  Unusual helical packing in crystals of DNA bearing a mutation hot spot. Nature. 341:459–462.
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Cazals F., Mueller C., Robert C., Roth A..  2013.  Towards Morse theory for point cloud data.. Inria Tech Reports.
Sterpone F, Derreumaux P, Melchionna S.  2016.  Toward Microscopic Simulations of Proteins in Cell-Like Environments. Biophys. J.. 110:386A.
Mazur AK.  1990.  Toward a theory of quasi-steady-state enzymatic processes. Mol. Biol.. 24:202–208.
Mazur AK.  2012.  Torque transfer coefficient in DNA under torsional stress. Phys. Rev. E. 86:011914.
Mazur AK.  2003.  Titration \em in silico of reversible B$łeftrightarrow$A transitions in DNA. J. Am. Chem. Soc.. 125:7849–7859.
Languin-Cattoën O, Melchionna S, Derreumaux P, Stirnemann G, Sterpone F.  2018.  Three Weaknesses for Three Perturbations: Comparing Protein Unfolding Under Shear, Force, and Thermal Stresses. J Phys Chem B. 122:11922-11930.
Tai K, Baaden M, Murdock S, Wu B, Ng MHong, Johnston S, Boardman R, Fangohr H, Cox K, Essex JW et al..  2007.  Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database. Journal of Molecular Graphics \& Modelling. 25:896–902.
Sterpone F, Melchionna S.  2012.  Thermophilic proteins: insight and perspective from in silico experiments. Chem. Soc. Rev.. 41:1665–1676.

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