Publications

2022

• Cerdan, A. H.; Peverini, L.; Changeux, J.-P.; Corringer, P.-J.; Cecchini, M., Lateral fenestrations in the extracellular domain of the glycine receptor contribute to the main chloride permeation pathway. Science Advances 2022, 8 (41).
• Bartocci, A.; Pereira, G.; Cecchini, M.; Dumont, E., Capturing the Recognition Dynamics of para-Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment. Journal of Chemical Information and Modeling 2022. 

2021

• Cecchini, M.; Changeux, J.-P., Nicotinic receptors: From protein allostery to computational neuropharmacology. Molecular Aspects of Medicine 2021, 84 (1), 101044.
• Sisquellas, M.; Cecchini, M., PrepFlow: A Toolkit for Chemical Library Preparation and Management for Virtual Screening. Molecular Informatics 2021, 40 (12), 2100139.
• Blanc, F. E., Cecchini, M., An Asymmetric Mechanism in a Symmetric Molecular Machine. Journal of Physical Chemistry Letters 2021, 12 (13), 3260-3265.
• Pereira, G.; Cecchini, M., Multibasin Quasi-Harmonic Approach for the Calculation of the Configurational Entropy of Small Molecules in Solution. Journal of Chemical Theory and Computation 2021, 17 (2), 1133–1142.

2020

• Cerdan, A. H.; Cecchini, M., On the Functional Annotation of Open-Channel Structures in the Glycine Receptor. Structure 2020, 28 (6), 690-693.e3.
• Montalvo-Acosta, J. J.; Dryzhakov, M.; Richmond, E.; Cecchini, M.; Moran, J., A Supramolecular Model for the Co-Catalytic Role of Nitro Compounds in Brønsted Acid Catalyzed Reactions.  Chemistry – A European Journal 2020, 26 (48), 10976.
• Cerdan, A. H.; Sisquellas, M.; Pereira, G.; Barreto Gomes, D. E., Changeux, J.-P.; Cecchini, M., The Glycine Receptor Allosteric Ligands Library (GRALL). Bioinformatics 2020, 36 (11), 3379-3384.

2019

• Wodak, S. J.; Paci, E.; Dokholyan, N.; Berezovsky, I. N.; Horovitz, A.; Li, J.; Hilser, V. J.; Bahar, I.; Karanicolas, J.; Stock, G.; Hamm, P.; Stote, R. H.; Eberhardt, J.; Chebaro, Y.; Dejaegere, A.; Cecchini, M.; Changeux, J. P.; Keri, D.; Barth, P.; Bolhuis, P. G.; Vreede, J.; Faccioli, P.; Orioli, S.; Ravasio, R.; Yan, L.; Brito, C.; Wyart, M.; Gkeka, P.; Rivalta, I.; Palermo, G.; McCammon, J. A.; Panecka-Hofman, J.; Wade, R.; Di Pizio, A.; Niv, M.; Nussinov, R.; Tsai C-J; Jang, H.; McLeish, T., Allostery in its many disguises: from theory to applications. Structure 2019.

2018

• Zeng, X.; Zhu, L.; Zheng, X.; Cecchini, M.; Huang, X., Harnessing complexity in molecular self-assembly using computer simulations. Physical Chemistry Chemical Physics : PCCP 2018, 20 (10), 6767-6776.
• Montalvo-Acosta, J. J.; Pacak, P.; Gomes, D. E. B.; Cecchini, M., A Linear Interaction Energy Model for Cavitand Host-Guest Binding Affinities. The Journal of Physical Chemistry. B 2018, 122 (26), 6810-6814.
• Conti, S.; Cecchini, M., Modeling the adsorption equilibrium of small-molecule gases on graphene: effect of the volume to surface ratio. Physical Chemistry Chemical Physics : PCCP 2018, 20 (15), 9770-9779.
• Cerdan, A. H.; Martin, N. E.; Cecchini, M., An Ion-Permeable State of the Glycine Receptor Captured by Molecular Dynamics. Structure 2018, 26 (11), 1555-1562 e4.
• Blanc, F.; Isabet, T.; Benisty, H.; Sweeney, H. L.; Cecchini, M.; Houdusse, A., An intermediate along the recovery stroke of myosin VI revealed by X-ray crystallography and molecular dynamics. Proceedings of the National Academy of Sciences of the United States of America 2018, 115 (24), 6213-6218.

2017

• Martin, N. E.; Malik, S.; Calimet, N.; Changeux, J. P.; Cecchini, M., Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics. PLoS Computational Biology 2017, 13 (10), e1005784.
• Harkat, M.; Peverini, L.; Cerdan, A. H.; Dunning, K.; Beudez, J.; Martz, A.; Calimet, N.; Specht, A.; Cecchini, M.; Chataigneau, T.; Grutter, T., On the permeation of large organic cations through the pore of ATP-gated P2X receptors. Proceedings of the National Academy of Sciences of the United States of America 2017, 114 (19), E3786-E3795.

2016

• Ropars, V.; Yang, Z.; Isabet, T.; Blanc, F.; Zhou, K.; Lin, T.; Liu, X.; Hissier, P.; Samazan, F.; Amigues, B.; Yang, E. D.; Park, H.; Pylypenko, O.; Cecchini, M.; Sindelar, C. V.; Sweeney, H. L.; Houdusse, A., The myosin X motor is optimized for movement on actin bundles. Nature Communications 2016, 7, 12456.
• Planelles-Herrero, V. J.; Blanc, F.; Sirigu, S.; Sirkia, H.; Clause, J.; Sourigues, Y.; Johnsrud, D. O.; Amigues, B.; Cecchini, M.; Gilbert, S. P.; Houdusse, A.; Titus, M. A., Myosin MyTH4-FERM structures highlight important principles of convergent evolution. Proceedings of the National Academy of Sciences of the United States of America 2016, 113 (21), E2906-15.
• Montalvo-Acosta, J. J.; Cecchini, M., Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding. Molecular Informatics 2016, 35 (11-12), 555-567.
• Melaccio, F.; Calimet, N.; Schapiro, I.; Valentini, A.; Cecchini, M.; Olivucci, M., Space and Time Evolution of the Electrostatic Potential During the Activation of a Visual Pigment. The Journal of Physical Chemistry Letters 2016, 7 (13), 2563-7.
• Habermacher, C.; Martz, A.; Calimet, N.; Lemoine, D.; Peverini, L.; Specht, A.; Cecchini, M.; Grutter, T., Photo-switchable tweezers illuminate pore-opening motions of an ATP-gated P2X ion channel. Elife 2016, 5, e11050.
• El Garah, M.; Dianat, A.; Cadeddu, A.; Gutierrez, R.; Cecchini, M.; Cook, T. R.; Ciesielski, A.; Stang, P. J.; Cuniberti, G.; Samori, P., Atomically Precise Prediction of 2D Self-Assembly of Weakly Bonded Nanostructures: STM Insight into Concentration-Dependent Architectures. Small 2016, 12 (3), 343-50.
• Conti, S.; del Rosso, M. G.; Ciesielski, A.; Weippert, J.; Bottcher, A.; Shin, Y.; Melinte, G.; Ersen, O.; Casiraghi, C.; Feng, X.; Mullen, K.; Kappes, M. M.; Samori, P.; Cecchini, M., Perchlorination of Coronene Enhances its Propensity for Self-Assembly on Graphene. ChemPhysChem 2016, 17 (3), 352-7.
• Conti, S.; Cecchini, M., Predicting molecular self-assembly at surfaces: a statistical thermodynamics and modeling approach. Physical chemistry chemical physics : PCCP 2016, 18 (46), 31480-31493.

2015

• Haar, S.; Ciesielski, A.; Clough, J.; Yang, H.; Mazzaro, R.; Richard, F.; Conti, S.; Merstorf, N.; Cecchini, M.; Morandi, V.; Casiraghi, C.; Samori, P., A supramolecular strategy to leverage the liquid-phase exfoliation of graphene in the presence of surfactants: unraveling the role of the length of fatty acids. Small 2015, 11 (14), 1691-702.
• Esque, J.; Cecchini, M., Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach. The Journal Physical Chemistry B. 2015, 119 (16), 5194-207.
• The journal physical chemistry B. Conti, S.; Cecchini, M., Accurate and Efficient Calculation of the Desorption Energy of Small Molecules from Graphene. The Journal Physical Chemistry C. 2015, 119 (4), 1867-1879.
• Cecchini, M.; Changeux, J. P., The nicotinic acetylcholine receptor and its prokaryotic homologues: Structure, conformational transitions & allosteric modulation. Neuropharmacology 2015, 96 (Pt B), 137-49.
• Cecchini, M., Quantum Corrections to the Free Energy Difference between Peptides and Proteins Conformers. The Journal of Chemical Theory and Computation 2015, 11 (9), 4011-22.
• Bonacchi, S.; El Garah, M.; Ciesielski, A.; Herder, M.; Conti, S.; Cecchini, M.; Hecht, S.; Samori, P., Surface-induced selection during in situ photoswitching at the solid/liquid interface. Angewandte Chemie 2015, 54 (16), 4865-9.

2014

• Taly, A.; Henin, J.; Changeux, J. P.; Cecchini, M., Allosteric regulation of pentameric ligand-gated ion channels: an emerging mechanistic perspective. Channels 2014, 8 (4), 350-60.

2013

 

• Ovchinnikov, V.; Cecchini, M.; Karplus, M., A simplified confinement method for calculating absolute free energies and free energy and entropy differences. The Journal of Physical Chemistry. B 2013, 117 (3), 750-62.
• Calimet, N.; Simoes, M.; Changeux, J. P.; Karplus, M.; Taly, A.; Cecchini, M., A gating mechanism of pentameric ligand-gated ion channels. Proceedings of the National Academy of Sciences of the United States of America 2013, 110 (42), E3987-96.