Publications

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Derreumaux P, ZHANG GH, SCHLICK T, BROOKS B.  1994.  A TRUNCATED NEWTON MINIMIZER ADAPTED FOR CHARMM AND BIOMOLECULAR APPLICATIONS. J. Comput. Chem.. 15:532–552.
Brunet YR, Hénin J, Celia H, Cascales E.  2014.  Type VI secretion and bacteriophage tail tubes share a common assembly pathway.. Embo Rep.. 15:315–21.
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Costa D., Garrain P.A, Baaden M.  2013.  Understanding small biomolecule-biomaterial interactions: a review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces. J. Biomed. Mater. Res. A. 101:1210–1222.
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.
Nguyent P, Derreumaux P.  2014.  Understanding Amyloid Fibril Nucleation and A beta Oligomer/Drug Interactions from Computer Simulations. Acc. Chem. Res.. 47:603–611.
Hénin J, Shinoda W, Klein ML.  2008.  United-Atom Acyl Chains for CHARMM Phospholipids. J. Phys. Chem. B.. 112:7008–7015.
Doutreligne S., Gageat C., Cragnolini T., Taly A, Pasquali S., Derreumaux P, Baaden M.  2015.  UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules. Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on. :1–6.
Doutreligne S., Cragnolini T., Pasquali S., Derreumaux P, Baaden M.  2014.  UnityMol: Interactive scientific visualization for integrative biology. Large Data Analysis and Visualization (LDAV), 2014 IEEE 4th Symposium on. :109–110.
Bullerjahn JTómas, von Bülow S, Heidari M, Hénin J, Hummer G.  2023.  Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation. 19:3406–3417.
CHHIBA M, Derreumaux P, VERGOTEN G.  1994.  THE USE OF THE SPASIBA SPECTROSCOPIC POTENTIAL FOR REPRODUCING THE STRUCTURES AND VIBRATIONAL FREQUENCIES OF A SERIES OF ACIDS - ACETIC-ACID, PIVALIC ACID, SUCCINIC ACID, ADIPIC ACID AND L-GLUTAMIC ACID. J. Mol. Struct.. 317:171–184.
LAGANT P, Derreumaux P, VERGOTEN G, PETICOLAS W.  1991.  THE USE OF ULTRAVIOLET RESONANCE RAMAN INTENSITIES TO TEST PROPOSED MOLECULAR-FORCE FIELDS FOR NUCLEIC-ACID BASES. J. Comput. Chem.. 12:731–741.
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.
Fiorin G, Klein ML, Hénin J.  2013.  Using collective variables to drive molecular dynamics simulations. Mol. Phys.. 111:3345–3362.
WILSON K.J, Derreumaux P, VERGOTEN G., Peticolas W.L.  1988.  Uv Resonance Raman-spectra and Solution State Conformations of Cholinergic Neurotransmitters. Biophys. J.. 53:A287-A287.
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Derreumaux P, VERGOTEN G, LAGANT P.  1990.  A VIBRATIONAL MOLECULAR-FORCE FIELD OF MODEL COMPOUNDS WITH BIOLOGICAL INTEREST .1. HARMONIC DYNAMICS OF CRYSTALLINE UREA AT 123-K. J. Comput. Chem.. 11:560–568.
Dauchez M, Derreumaux P, VERGOTEN G.  1993.  VIBRATIONAL MOLECULAR-FORCE FIELD OF MODEL COMPOUNDS WITH BIOLOGIC INTEREST .2. HARMONIC DYNAMICS OF BOTH ANOMERS OF GLUCOSE IN THE CRYSTALLINE STATE. J. Comput. Chem.. 14:263–277.
Dauchez M, Derreumaux P, LAGANT P, VERGOTEN G.  1995.  A VIBRATIONAL MOLECULAR-FORCE FIELD OF MODEL COMPOUNDS WITH BIOLOGICAL INTEREST .4. PARAMETERS FOR THE DIFFERENT GLYCOSIDIC LINKAGES OF OLIGOSACCHARIDES. J. Comput. Chem.. 16:188–199.
Krone M., Kozlikova B., Lindow N., Baaden M, Baum D., Parulek J., Hege H.-C., Viola I..  2016.  Visual Analysis of Biomolecular Cavities: State of the Art. Comput. Graphics Forum. 35:527–551.
Férey N, Gros P.-E., Hérisson J., Gherbi R..  2005.  Visual data mining of genomic databases by immersive graph-based exploration. international Conference on Computer Graphics and interactive Techniques in Australasia and South East Asia (GRAPHITE 2005 - ACM-ACMSIGRAPH Sponsored). :143–146.
Férey N, Gherbi R..  2006.  Visual Mining for Microarray Knowledge Discovery. International Conference on Information & Communication Technologies: from Theory to Applications (ICTTA 2006 - IEEE).
Férey N, Gros P.-E., Hérisson J., Gherbi R..  2004.  Visualization and Exploration of Factual and Textual Genomic Data. Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM 2004).
Kozlikova B, Krone M, Lindow N, Falk M, Baaden M, Baum D, Viola I, Parulek J, Hege H-C.  2015.  Visualization of Biomolecular Structures: State of the Art. Eurographics Conference on Visualization (EuroVis) - STARs.
Kozlikova B., Krone M., Falk M., Lindow N., Baaden M, Baum D., Viola I., Parulek J., Hege H.-C..  2016.  Visualization of Biomolecular Structures: State of the Art Revisited. Comput. Graphics Forum.
Kozlikova B., Krone M., Falk M., Lindow N., Baaden M, Baum D., Viola I., Parulek J., Hege H.-C..  2017.  Visualization of Biomolecular Structures: State of the Art Revisited: Visualization of Biomolecular Structures. Computer Graphics Forum. 36:178–204.
Baaden M.  2019.  Visualizing Biological Membrane Organization and Dynamics.. J Mol Biol. 431(10):1889-1919.

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