Publications

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2024
Versini R., Sritharan S., B. Fas A, Tubiana T., Aimeur S.Z, Henri J., Erard M., Nüsse O., Andreani J., Baaden M. et al..  2024.  A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model. 64:26–41.
Versini R., Sritharan S., B. Fas A, Tubiana T., Aimeur S.Z, Henri J., Erard M., Nüsse O., Andreani J., Baaden M. et al..  2024.  A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model. 64:26–41.
2023
Dragelj J, Karafoulidi-Retsou C, Katz S, Lenz O, Zebger I, Caserta G, Sacquin-Mora S, Mroginski MAndrea.  2023.  Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator. Frontiers in Microbiology. 13
Gagelin A, Largeau C, Masscheleyn S, Piel MS, Calderón-Mora D, Bouillaud F, Hénin J, Miroux B.  2023.  Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling.. Nat Commun. 14(1):2594.
2022
Puyo-Fourtine J, Juillé M, Hénin J, Clavaguéra C, Duboué-Dijon E.  2022.  Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J. Phys. Chem. B. 126(22):4022-4034.
Spalvieri D, Mauviel A-M, Lambert M, Férey N, Sacquin-Mora S, Chavent M, Baaden M.  2022.  Design – a new way to look at old molecules. Journal of Integrative Bioinformatics. 19:20220020.
Chávez-García C, Hénin J, Karttunen M.  2022.  Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2.. J Chem Inf Model. 62(4):958-970.
Petroff JT, Dietzen NM, Santiago-McRae E, Deng B, Washington MS, Chen LJ, K. Moreland T, Deng Z, Rau M, Fitzpatrick JAJ et al..  2022.  Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications. 13
Petroff JT, Dietzen NM, Santiago-McRae E, Deng B, Washington MS, Chen LJ, K. Moreland T, Deng Z, Rau M, Fitzpatrick JAJ et al..  2022.  Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications. 13
O'Donnell T, Robert CH, Cazals F.  2022.  Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions. Proteins: Structure, Function, and Bioinformatics. 90:858-868.
2021
Wu X, Hénin J, Baciou L, Baaden M, Cailliez F, de la Lande A.  2021.  Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations.. Front Chem. 9:650651.
2020
Hung HMinh, Nguyen MTho, Tran P-T, Truong VKhanh, Chapman J, Anh LHuu Quynh, Derreumaux P, Vu VV, Ngo STung.  2020.  Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ Peptide.. J Chem Inf Model. 60(3):1399-1408.
Phillips J, Hardy D, Maia J, Stone J, Ribeiro J, Bernardi R, Buch R, Fiorin G, Hénin J, Jiang W et al..  2020.  Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153
Martinez X, Chavent M, Baaden M.  2020.  Visualizing protein structures - tools and trends.. Biochem Soc Trans.
2019
Esmenjaud J-B, Stroebel D, Chan K, Grand T, David M, Wollmuth LP, Taly A, Paoletti P.  2019.  An inter-dimer allosteric switch controls NMDA receptor activity. The EMBO journal. 38
Martinez X, Krone M, Alharbi N, Rose AS, Laramee RS, O'Donoghue S, Baaden M, Chavent M.  2019.  Molecular Graphics: Bridging Structural Biologists and Computer Scientists.. Structure. 27(11):1617-1623.
De Vecchis D, Brandner A, Baaden M, Cohen MM, Taly A.  2019.  A molecular perspective on mitochondrial membrane fusion: from the key players to oligomerization and tethering of mitofusin. The Journal of membrane biology. 252:293–306.
Chiricotto M, Melchionna S, Derreumaux P, Sterpone F.  2019.  Multiscale Aggregation of the Amyloid Aβ16–22 Peptide: From Disordered Coagulation and Lateral Branching to Amorphous Prefibrils. The Journal of Physical Chemistry Letters. 10:1594-1599.
Brandner A, De Vecchis D, Baaden M, Cohen MM, Taly A.  2019.  Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking. Mitochondrion. 49:234–244.
Brandner A, De Vecchis D, Baaden M, Cohen MM, Taly A.  2019.  Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking.. Data Brief. 26:104460.
Nguyen PHoang, Campanera JM, Ngo STung, Loquet A, Derreumaux P.  2019.  Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution.. J Phys Chem B. 123(31):6750-6756.
Nguyen PHoang, Campanera JM, Ngo STung, Loquet A, Derreumaux P.  2019.  Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane.. J Phys Chem B. 123(17):3643-3648.
2018
Baaden M, Barboiu M, Borthakur MPratim, Chen C-L, Coalson R, Davis J, Freger V, Gong B, Hélix-Nielsen C, Hickey R et al..  2018.  Applications to water transport systems: general discussion.. Faraday Discuss. 209:389-414.
Baaden M, Barboiu M, Borthakur MPratim, Chen C-L, Coalson R, Davis J, Freger V, Gong B, Hélix-Nielsen C, Hickey R et al..  2018.  Applications to water transport systems: general discussion.. Faraday Discuss. 209:389-414.
Baaden M, Barboiu M, Bill RM, Chen C-L, Davis J, Di Vincenzo M, Freger V, Fröba M, Gale PA, Gong B et al..  2018.  Biomimetic water channels: general discussion.. Faraday Discuss. 209:205-229.

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