Seeber, M., Felline, A., Raimondi, F., Muff, S., Friedman, R., Rao, F., … Fanelli, F. (2011). Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry, 32(6), 1183-1194. https://doi.org/10.1002/jcc.21688 (Original work published)

Qi, B., Muff, S., Caflisch, A., & Dinner, A. R. (2010). Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. The Journal of Physical Chemistry B, 114(20), 6979-6989. https://doi.org/10.1021/jp101476g (Original work published)

Kaiser-Bunbury, C. N., Muff, S., Memmott, J., Müller, C. B., & Caflisch, A. (2010). The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour. Ecology Letters, 13(4), 442-52. https://doi.org/10.1111/j.1461-0248.2009.01437.x (Original work published 2010)

Muff, S., & Caflisch, A. (2009). Identification of the protein folding transition state from molecular dynamics trajectories. Journal of Chemical Physics, 130(12), 125104. https://doi.org/10.1063/1.3099705 (Original work published)

Muff, S., & Caflisch, A. (2009). ETNA: Equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations. The Journal of Physical Chemistry B, 113(10), 3218-3226. https://doi.org/10.1021/jp807261h (Original work published)

Krivov, S. V., Muff, S., Caflisch, A., & Karplus, M. (2008). One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: New insights into the folding process. The Journal of Physical Chemistry B, 112(29), 8701-8714. https://doi.org/10.1021/jp711864r (Original work published)

Ihalainen, J. A., Paoli, B., Muff, S., Backus, E. H. G., Bredenbeck, J., Woolley, G. A., … Hamm, P. (2008). Alpha-Helix folding in the presence of structural constraints. Proceedings of the National Academy of Sciences of the United States of America, 105(28), 9588-9593. https://doi.org/10.1073/pnas.0712099105 (Original work published)

Muff, S., & Caflisch, A. (2008). Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein. Proteins: Structure, Function, and Bioinformatics, 70(4), 1185-1195. https://doi.org/10.1002/prot.21565 (Original work published 2008)

Muff, S., Rao, F., & Caflisch, A. (2005). Local modularity measure for network clusterizations. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics, 72(5.2), 056107. https://doi.org/10.1103/PhysRevE.72.056107 (Original work published 2005)