Reference Websites


Google Scholar

Research Gate

Publications List

M. A. Cuendet, O. Michielin, 2020, “Digitalization Is Fueling a Revolution in Precision Oncology”, in Reference Module in Biomedical Sciences, Elsevier (2020)

F. Martins, L. Schiappacasse, M. Levivier, C. Tuleasca, M. A. Cuendet, V. Aedo-Lopez, B. Gautron Moura, K. Homicsko, A. Bettini, G. Berthod, C. L. Gérard, A. Wicky, J. Bourhis, O. Michielin, “The combination of stereotactic radiosurgery with immune checkpoint inhibition or targeted therapy in melanoma patients with brain metastases: a retrospective study”, J. Neuro-Onco. 146(1) : 181 (2020)

M. A. Cuendet, Y. Liu, L. Goffin, R. Šachl, M. Cebecauer, L. Cariolato, P. Guillaume, P. Reichenbach, M. Irving, G. Coukos, I. F. Luescher, “CD8 Binding of MHC-Peptide Complexes in cis or trans Regulates CD8+ T-cell Responses”,J. Mol. Biol. 431(24) : 4941 (2019)

H. Carrillo-Cabada, J. Benson, A. Razavi, B. Mulligan, M. A Cuendet, H. Weinstein, M. Taufer, T. Estrada, “A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes”,IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10.1109/TCBB.2019.2945291 (2019)

M. A. Cuendet, D. Margul, E. Schneider, M. E. Tuckerman, "Endpoint-restricted adiabatic free energy dynamics approach for the exploration of biomolecular conformational equilibria", J. Chem. Phys. 149(7) : 072316 (2018)

P. S. Merkle, K. Gotfryd,*, M. A. Cuendet, K. Z. Leth-Espensen, U. Gether, C. J. Loland, K. D. Rand, "Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT", Science Advances 4(5) : eaar6179 (2018)

M. Doktorova, F. A. Heberle, R. L. Kingston, G. Khelashvili, M. A. Cuendet, Y. Wen, J. Katsaras, G. W. Feigenson, V. M. Vogt, R. A. Dick, “Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties” Biophys. J. 113(9) : 2004 (2017)

M. V. LeVine, M. A. Cuendet, A. M. Razavi, G. Khelashvili, H. Weinstein, “Thermodynamic Coupling Function Analysis of Allosteric Mechanisms in the Human Dopamine Transporter”, Biophysical J. 114(1) : 10 (2017)

P. S. Merkle, M. Irving, S. Hongjian, M. Ferber, T. J. D. Jørgensen, K. Scholten, I. Luescher, G. Coukos, V. Zoete, M. A. Cuendet, O. Michielin, K. D. Rand, “The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites”, Biochemistry, 56(30) : 3945 (2017)

M. A. Cuendet, H. Weinstein, M. V. LeVine, “The Allostery Landscape: Quantifying Thermodynamic Couplings in Biomolecular Systems”, J. Chem. Theory Comput. 12(12) : 5758 (2016)

M. V. LeVine, M. A. Cuendet, G. Khelashvili, H. Weinstein, "Allosteric Mechanisms of Molecular Machines at the Membrane: Transport by Sodium-Coupled Symporters", Chem. Rev. 116(11) : 6552. (2016)

N. Akyuz, E. R. Georgieva, Z. Zhou, S. Stolzenberg, M. A. Cuendet, G. Khelashvili, R. B. Altman, D. S. Terry, J. H. Freed, H. Weinstein, O. Boudker, S. C. Blanchard, "Transport domain unlocking sets the uptake rate of an aspartate transporter", Nature 518(7537) : 68-73 (2015)

M. A. Cuendet, M. E. Tuckerman, "Free energy reconstruction from metadynamics or adiabatic free energy dynamics simulations", J. Chem. Theory Comput. 10(8) : 2975 (2014)

M. A. Cuendet, A. T. Tzanov (co-first author), M. E. Tuckerman, "How accurately do current force fields predict experimental peptide conformations? An adiabatic free energy dynamics study", J. Phys. Chem. B, 118 (24) : 6539 (2014)

V. Zoete, M. Irving, M. Ferber, M. A. Cuendet, O. Michielin, "Structure-based, rational design of T cell receptors", Frontiers in Immunology 4(268) (2013)

M. A. Cuendet and M. E. Tuckerman, “Alchemical free energy differences in flexible molecules from thermodynamic integration or free energy perturbation combined with driven adiabatic dynamics”, J. Chem. Theory Comput. 8(10) : 3504 (2012)

M. Chen, M. A. Cuendet, and M. E. Tuckerman, “Heating and flooding: A unified approach for rapid generation of free energy surfaces”, J. Chem. Phys., 137 : 024102 (2012)

M. A. Cuendet, V. Zoete, O. Michielin, "How T cell receptors interact with peptide-MHCs: A multiple steered molecular dynamics study", Proteins Struct. Funct. Bioinfo. 79 (11) : 3007 (2011)

V. Zoete, M. A. Cuendet, A. Grosdidier, O. Michielin, "SwissParam, a Fast Force Field Generation Tool For Small Organic Molecules", J. Comput. Chem. 32 (11) : 2359 (2011)

V. Zoete, A. Grosdidier, M. A. Cuendet and O. Michielin, "Use of the FACTS solvation model for protein–ligand docking calculations. Application to EADock", J. Mol. Recognit. 23 : 457 (2010)

P. Bjelkmar, P. Larsson, M. A. Cuendet, B. Hess and E. Lindahl, "Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models", J. Chem. Theory Comput. 6(2) : 459 (2010)

V. Zoete, M. A. Cuendet, U. F. Roehrig, A. Grosdidier and O. Michielin, "Molecular Modeling of Proteins: From Simulations to Drug Design Applications", in Bioinformatics, A Swiss Perspective (R. D. Appel and E. Feytmans, eds.), World Scientific Publishing (2009)

M. A. Cuendet, O. Michielin, "Protein-Protein Interaction Investigated by Steered Molecular Dynamics: the TCR-pMHC Complex", Biophysis J. 95(8) : 1 (2008)

M. A. Cuendet, V. Zoete, and O. Michielin, "Molecular dynamics-based free energy simulations", in Computational Structural Biology (T. Schwede and M. Peitsch, eds.), World Scientific Publishing (2008)

M. A. Cuendet, W. F. van Gunsteren, "On the calculation of velocity-dependent properties in molecular dynamics simulations using the leap-frog integration algorithm", J. Chem. Phys. 127, 184102 (2007)

M. Cascella, M. A. Cuendet, I. Tavernelli, U. Rothlisberger, "Optical Spectra of Cu(II)-Azurin by Hybrid TDDFT-Molecular Dynamics Simulations", J. Phys. Chem. B, 111(34) : 10248 -10252 (2007)

M. A. Cuendet, "The Jarzynski identity derived from general Hamiltonian or non-Hamiltonian dynamics reproducing NVT or NPT ensembles", J. Chem. Phys. 125 : 144109 (2006)

M. A. Cuendet, "Statistical mechanical derivation of the Jarzynski identity for non-Hamiltonian thermostated dynamics", Phys. Rev. Lett. 96(1) : 120602 (2006).

A. Labbi, M. Cuendet, "Predictive Data Mining for Project Portfolio Risk Management" in "Handbook of Integrated Risk Management for E-Business : Measuring, Modeling, and Managing Risk", J. Ross Publishing (2005), p. 151 (ISBN 193215907X).

M. Cuendet, A. Labbi, "Consistent AdaBoost for boosting stumps", Proceedings of the International Conference on Machine Learning and Applications - ICMLA 2002, Las Vegas, Nevada, USA. CSREA Press (2002) p. 117.

M. Cuendet, A. Labbi, "Some theoretical and practical perspectives on boosting weak predictors", IBM Research technical paper RZ3402 (2002).

A.Labbi, M. Cuendet, "Boosted decision trees for project risk assessment and pricing", IBM Research technical paper RZ340 (2002).