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Seeber, M., Cecchini, M., Rao, F., Settanni, G., & Caflisch, A. (2007). Wordom: A program for efficient analysis of molecular dynamics simulations. Bioinformatics, 23(19), 2625-2627. https://doi.org/10.1093/bioinformatics/btm378 (Original work published)

Gfeller, D., De Los Rios, P., Caflisch, A., & Rao, F. (2007). Complex network analysis of free-energy landscapes. Proceedings of the National Academy of Sciences of the United States of America, 104(6), 1817-1822. https://doi.org/10.1073/pnas.0608099104 (Original work published)

Rao, F., Settanni, G., & Caflisch, A. (2007). Estimation of folding probabilities and Phi values from molecular dynamics simulations of reversible peptide folding. In Y. Bai & R. Nussinov (Eds.), Protein Folding Protocols (pp. 225-249). Totowa, NJ: Humana Press, Inc. https://doi.org/10.1385/1-59745-189-4:225

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)

Rao, F., Settanni, G., Guarnera, E., & Caflisch, A. (2005). Estimation of protein folding probability from equilibrium simulations. Journal of Chemical Physics, 122(18), 184901. https://doi.org/10.1063/1.1893753 (Original work published)

Settanni, G., Rao, F., & Caflisch, A. (2005). Phi-value analysis by molecular dynamics simulations of reversible folding. Proceedings of the National Academy of Sciences of the United States of America, 102(3), 628-633. https://doi.org/10.1073/pnas.0406754102 (Original work published)

Rao, F., & Caflisch, A. (2003). Replica exchange molecular dynamics simulations of reversible folding. The Journal of Chemical Physics, 119(7), 4035-4042. https://doi.org/10.1063/1.1591721

Rao, F., & Caflisch, A. (2004). The protein folding network. Journal of Molecular Biology, 342(1), 299-306. https://doi.org/10.1016/j.jmb.2004.06.063 (Original work published)

Cecchini, M., Rao, F., Seeber, M., & Caflisch, A. (2004). Replica exchange molecular dynamics simulations of amyloid peptide aggregation. Journal of Chemical Physics, 121(21), 10748-10756. https://doi.org/10.1063/1.1809588 (Original work published)