Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., … Karplus, M. (2024). CHARMM at 45: Enhancements in accessibility, functionality, and speed. The Journal of Physical Chemistry B, X. https://doi.org/10.1021/acs.jpcb.4c04100 (Original work published)

Kalgin, I. V., Caflisch, A., Chekmarev, S. F., & Karplus, M. (2013). New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: Application to a hydrodynamic analysis of the folding flow. The Journal of Physical Chemistry B, 117(20), 6092-6105. https://doi.org/10.1021/jp401742y (Original work published)

Brooks, B. R., Brooks III, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545-1614. https://doi.org/10.1002/jcc.21287 (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)

Caflisch, A., Fischer, S., & Karplus, M. (1997). Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP—substrate complex. Journal of Computational Chemistry, 18(6), 723–743. https://doi.org/10.1002/(SICI)1096-987X(19970430)18:6<723::AID-JCC1>3.0.CO;2-U

Paci, E., Caflisch, A., Plückthun, A., & Karplus, M. (2001). Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. Journal of Molecular Biology, 314(3), 589-605. https://doi.org/10.1006/jmbi.2001.5103 (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., & Karplus, M. (1999). Structural details of urea binding to barnase: A molecular dynamics analysis. Structure, 7(5), 477-488. https://doi.org/doi:10.1016/S0969-2126(99)80064-1 (Original work published 1999)

Caflisch, A., & Karplus, M. (1995). Computational combinatorial chemistry for de novo ligand design: Review and assessment. Perspectives in Drug Discovery and Design, 3(1), 51-84. https://doi.org/10.1007/BF02174467

Caflisch, A., & Karplus, M. (1995). Acid and thermal denaturation of barnase investigated by molecular dynamics simulations. Journal of Molecular Biology, 252(5), 672-708. https://doi.org/10.1006/jmbi.1995.0528 (Original work published)