Talks, Posters or Abstracts at Scientific Conferences

M. A. Cuendet, M. V. LeVine, H. Weinstein,  "Landscapes of Allostery: Thermodynamic Coupling Function Analysis to Characterize Allosteric Mechanisms in Proteins", CECAM Workshop: Multiscale Simulations of Allosteric Regulatory Mechanisms in Cancer-associated Proteins and Signaling Protein Networks, Lugano, October 15-17, 2018.

T. Estrada, J. Benson, H. Carrillo-Cabada, A. M. Razavi, M. A. Cuendet, H. Weinstein, E. Deelman, M. Taufer, “Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis”, Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, p. 315-324, Washington DC, Aug. 29 – Sept. 1, 2018.

K. Homicsko, M. A Cuendet, O. Michielin, "Serum protein predictors of long term survival from combined ipilimumab and nivolumab therapy in metastatic melanoma patients", J. Clinical Oncology 36 (15_suppl) : e21513 (2018), 2018 ASCO Annual Meeting, June 1, 2018.

M. V. LeVine, M. A. Cuendet, A. M. Razavi, G. Khelashvili, H. Weinstein, "Thermodynamic Coupling Function Analysis of Allosteric Coupling between Na+ Release and Inward-Opening in the Human Dopamine Transporter", Biophys. J.  114(3) : 421a (2018), 62th Biophysical Society Annual Meeting, San Fransisco (USA), Feb. 2, 2018.

K. Homicsko, M. A. Cuendet, A. Mlynska, B. Moura, C. Horak, D. Hanahan, O. Michielin, "Exploratory analysis of multiprotein serum predictors at baseline of progression-free survival of ipilimumab or ipilimumab and nivolumab in the Checkmate-069 study", (poster), 2017 ASCO Annual Meeting, June 3, 2017.

J. Sadek, A. Hauenstein, M. A. Cuendet, H. Weinstein, H. Wu, F. Glickman, E. Cesarman, “Targeting vFLIP for the treatment of KSHV-associated diseases: Losing NEMO interaction”, 20th International Workshop on Kaposi’s Sarcoma Herpes Virus (KSHV) and Related Agents, Berlin (Germany), July 25-28, 2017.

H. Weinstein, G. Khelashvili, M. V. LeVine, M. A. Cuendet, “Rigorous Representation of Transporters as Allosteric Machines Enables a Quantitative Understanding of their Functional Mechanisms”, Biophys. J. 112 (3), 308a (2017), 61th Biophysical Society Annual Meeting, New Orleans (USA), Feb. 11-15, 2017.

M. A. Cuendet, H. Weinstein, M. V. LeVine, “The Allostery Landscape: Quantifying Thermodynamic Couplings in Biomolecular Systems”, Biophys. J. 112 (3) : 354a (2017), 61th Biophysical Society Annual Meeting, New Orleans (USA), Feb. 11-15, 2017.

D. M Shore, D. B. Iaea, R. Rusinova, G. Khelashvili, M. A. Cuendet, O. S. Andersen, F. R. Maxfield, H. Weinstein, “Vectorial Cholesterol Transport by STARD4 is Mediated by Specific PIP2 Membrane Composition”, Biophys. J. 112 (3) : 87a (2017),  61th Biophysical Society Annual Meeting, New Orleans (USA), Feb. 11-15, 2017.

M. A. Cuendet, H. Weinstein, "Dissecting Functional Correlates of a Double Mutation Enhancing GltPh Transport Efficiency using Alchemical Free Energy Calculations", Biophys. J., 3 Suppl. 1(110), 627a (2016), (poster), 60th Biophysical Society Annual Meeting, Los Angeles (USA), Feb. 27 - Mar. 02, 2016.

M. V. LeVine, M. A. Cuendet, G. Khelashvili, H. Weinstein, "From Physics to Phenotype: New Insights into Allosteric Transport Mechanisms in LeuT", Biophys. J. 110(3) : 362a (2016), 60th Biophysical Society Annual Meeting, Los Angeles (USA),  Feb. 27 - Mar. 02, 2016.

M. A. Cuendet, S. Stolzenberg, G. Khelashvili, H. Weinstein, "Molecular Dynamics Simulation Study of a Mutant Construct of the Archaeal Glutamate Transporter GltPh with Transport Rates as Fast as its Human Counterpart", (platform presentation) Biophys. J. 108(2) : 198a (2015), 59th Biophysical Society Annual Meeting, Baltimore (USA), Feb 7-11 2015

M. A. Cuendet, "Using the Density and/or the Force for Free Energy Reconstruction from Medadynamics or Adiabatic Free Energy Dynamics Simulations" (poster), Workshop on Free Energy Methods in Drug Design, Vertex Pharmaceuticals, Boston (USA), Mai 19-21, 2014

M. A. Cuendet, "On the Geometry of Collective Variables and Artificial Entropic Pitfalls in Free Energy Calculations", CECAM Workshop on Entropy in Biomolecular Systems, University of Vienna, Vienna (Austria), Mai 14-17, 2014 (organizer of the conference)

M. A. Cuendet, "Re-weighting the Adiabatic Ensemble", Navigating Chemical Compound Space for Materials and Bio Design Reunion Conference, Institute for Pure and Applied Mathematics, Lake Arrowhead (USA), Dec 9-14, 2012

M. A. Cuendet, M. E. Tuckerman, "Adiabatic Free Energy Methods", Exploring Protein Interactions through Theory and Experiments, CECAM, Lausanne (Switzerland), September 24-26, 2012

M. A. Cuendet, M. E. Tuckerman, "Driven Adiabatic Free Energy Dynamics", ESF Conference on Energy Landscapes, Obergurgl (Austria), July 19, 2012

M. A. Cuendet, M. E. Tuckerman, “Adiabatic Free Energy Dynamics”, 2012 Workshop on Free Energy Methods in Drug Design, Cambridge (USA), May 23, 2012

M. A. Cuendet, M. E. Tuckerman, “Exploring the conformational space of the Trpzip2 peptide”, Navigating Chemical Compound Space for Materials and Bio Design Workshop, Institute for Pure and Applied Mathematics, Lake Arrowhead (USA), June 16, 2011

M. A. Cuendet, "Dissecting Protein-Protein Interactions and Side Chain Cooperativity", Navigating Chemical Compound Space for Materials and Bio Design Workshop, Institute for Pure and Applied Mathematics, UCLA (USA), May 20, 2011

M. A. Cuendet, O. Michielin, "How two different TCRs bind to the same peptide-MHC" (poster), Gordon Conference on Computational Chemistry, Les Diablerets (CH), Aug. 29 - Sept. 3, 2010

M. A. Cuendet, "Molecular dynamics on the grid", Swiss Grid Day, Bern (CH), Nov. 26, 2009

M. A. Cuendet, "Protein-protein recognition investigated using steered MD ... and a note on using thermostats in Gromacs", Workshop on Gromacs and Advanced Simulation Methods, MPI Goettingen, Germany, September 24-26, 2008

M. A. Cuendet, "Aspects of protein-protein recognition", Entropy in Biomolecular Systems, MedILS, Split (Croatia), August 10-16, 2008 (organizer of the conference)

M. A. Cuendet, "Aspects of nonautonaumous molecular dynamics", Classical and Quantum Approaches in Molecular Modeling, University of Minnesota, Minneapolis (USA), July 28, 2007.

M. A. Cuendet, "Aspects of nonequilibrium molecular dynamics", First Maxwell Institute Colloquium on Applications of Mathematics, University of Edinburgh (UK), November 23, 2006.

M. A. Cuendet, O. Michielin, "A steered molecular dynamics study of the TCR-pMHC complex" (poster), Gordon Research Conference on Computational Chemistry, Les Diablerets (CH), October 8-13, 2006.

M. A. Cuendet, "Derivation of the Jarzynski identity for non-Hamiltonian thermostated dynamics", CECAM Workshop: Theory of single molecule force experiments and simulations, Lyon (F), September 26-29, 2006.

M. A. Cuendet, "Statistical mechanical derivation of the Jarzynski identity for thermostated dynamics", (talk for the first poster price), 367. WE-Heraeus-Seminar: Biomolecular Simulation: From Physical Principles to Biological Function, Bad Honnef (D), May 22-24, 2006.

M. A. Cuendet, "Binding free energy profiles of specific immune recognition complexes", High performance computing for the life sciences (2nd Annual Vital-IT Symposium), Geneva (CH), April 7, 2006.

M. A. Cuendet, "Association free energy profile of the TCR-pMHC complex determined by steered molecular dynamics", Computer Simulation and Theory of Macromolecules, Hünfeld (D), May 19-21, 2005.

M. A. Cuendet, "A statistical mechanical proof of the Jarzynski identity, ... and little remarks about Gromacs", 15th Annual BIOMOS Meeting, Burg Arras (D), August 31, 2005.

M. A. Cuendet, A. Labbi, "Predictive Analysis for Project Portfolio Risk Management", Tenth International Congress on Computational and Applied Mathematics ICCAM, Leuven (BE), 2002.