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Friedman, R., & Caflisch, A. (2010). On the orientation of the catalytic dyad in aspartic proteases. Proteins, 78(6), 1575-1582. https://doi.org/10.1002/prot.22674 (Original work published)

Friedman, R., & Caflisch, A. (2009). Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. ChemMedChem, 4(8), 1317-1326. https://doi.org/10.1002/cmdc.200900078 (Original work published 2009)

Friedman, R., & Caflisch, A. (2008). Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins: Structure, Function, and Bioinformatics, 73(4), 814-827. https://doi.org/10.1002/prot.22105 (Original work published 2008)

Zhou, T., Huang, D., & Caflisch, A. (2008). Is quantum mechanics necessary for predicting binding free energy? Journal of Medicinal Chemistry, 51(14), 4280-4288. https://doi.org/10.1021/jm800242q (Original work published)

Friedman, R., & Caflisch, A. (2007). The protonation state of the catalytic aspartates in plasmepsin II. FEBS Letters, 581(21), 4120-4124. https://doi.org/10.1016/j.febslet.2007.07.033 (Original work published)

Gorfe, A. A., & Caflisch, A. (2005). Functional plasticity in the substrate binding site of beta-secretase. Structure, 13(10), 1487-1498. https://doi.org/10.1016/j.str.2005.06.015 (Original work published 2005)

Huang, D., Lüthi, U., Kolb, P., Edler, K., Cecchini, M., Audetat, S., … Caflisch, A. (2005). Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations. Journal of Medicinal Chemistry, 48(16), 5108-5111. https://doi.org/10.1021/jm050499d (Original work published)

Caflisch, A., Schramm, H. J., & Karplus, M. (2000). Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach. Journal of Computer-Aided Molecular Design, 14(2), 161-179. https://doi.org/10.1023/A:1008146201260 (Original work published 2000)

Caflisch, A., Miranker, A., & Karplus, M. (1993). Multiple copy simultaneous search and construction of ligands in binding sites: Application to inhibitors of HIV-1 aspartic proteinase. Journal of Medicinal Chemistry, 36(15), 2142-2167. (Original work published)