Cocina, F., Vitalis, A., & Caflisch, A. (2020). SAPPHIRE-based clustering. Journal of Chemical Theory and Computation, 16(10), 6383–6396. https://doi.org/10.1021/acs.jctc.0c00604 (Original work published)

Scalco, R., & Caflisch, A. (2011). Equilibrium distribution from distributed computing (simulations of protein folding). The Journal of Physical Chemistry B, 115(19), 6358-6365. https://doi.org/10.1021/jp2014918 (Original work published)

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)

Zhou, T., Lafleur, K., & Caflisch, A. (2010). Complementing ultrafast shape recognition with an optical isomerism descriptor. Journal of Molecular Graphics and Modelling, 29(3), 443-449. https://doi.org/10.1016/j.jmgm.2010.08.007 (Original work published 2010)

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)

Dey, F., & Caflisch, A. (2008). Fragment-based de novo ligand design by multiobjective evolutionary optimization. Journal of Chemical Information and Modeling, 48(3), 679-690. https://doi.org/10.1021/ci700424b (Original work published 2008)

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)

Budin, N., Ahmed, S., Majeux, N., & Caflisch, A. (2001). An evolutionary approach for structure-based design of natural and non-natural peptidic ligands. Combinatorial Chemistry & High Throughput Screening, 4(8), 661-673. https://doi.org/10.2174/1386207013330652 (Original work published 2001)

Budin, N., Majeux, N., & Caflisch, A. (2001). Fragment-based flexible ligand docking by evolutionary optimization. Biological Chemistry, 382(9), 1365-1372. https://doi.org/10.1515/BC.2001.168 (Original work published 2001)

Cavalli, A., Haberthür, U., Paci, E., & Caflisch, A. (2003). Fast protein folding on downhill energy landscape. Protein Science, 12(8), 1801-1803. https://doi.org/10.1110/ps.0366103 (Original work published 2003)