The CHARMM Generalized Force Field (CGenFF)

Daniel M. Rosenbaum, D.M, Cheng Zhang, C., Joseph Lyons, J., Ralph Holl, R., David Aragao, D, Daniel H. Arlow, D.H., Søren G. F. Rasmussen, S.G.F., Hee-Jung Choi, H.-H., Brian T. DeVree, B.T., Roger K. Sunahara, R.K., Pil Seok Chae, P.S., Samuel H. Gellman, S.H., Ron O. Dror, R.O., David E. Shaw, D.E., William I. Weis, W.I., Martin Caffrey, M., Peter Gmeiner, P. and Brian K. Kobilka, B.K., “Structure and Function of an Irreversible Agonist-β2 Adrenoceptor complex,” Nature, 469: 236-240, PMC3074335

Rais, R., Acharya, C., Tririya, G, MacKerell, Jr., A.D.,* and Polli, J.* "Molecular Switch Controlling the Binding of Anionic Bile Acid Conjugates to hASBT," Journal of Medicinal Chemistry, 53: 4749-4760, 2010, PMC2891776

Huang, D., Caflisch, A., “The Free Energy Landscape of Small Molecule Unbinding.” PLoS Computional Biology, 7: e1002002, 2011 doi:10.1371/journal.pcbi.1002002

Nowosielski, M., Hoffmann, M., Wyrwicz, L.S., Stepniak, P., Plewczynski, D.M., Lazniewski, M., Ginalski, K., Rychlewski, L., “Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine,” Journal of Chemical Information and Modeling, 51, 455–462, 2011, doi:10.1021/ci100403b

Morozov, A.N., D’Cunha, C., Alvarez, C.A., and Chatfield, D.C., “Enantiospecificity of Chloroperoxidase-Catalyzed Epoxidation: Biased Molecular Dynamics Study of a Cis-beta-Methylstyrene/Chloroperoxidase-Compound I Complex,” Biophysical Journal, 100, 1066–1075, 2011, doi:10.1016/j.bpj.2010.12.3729

Raman, E.P., Yu, W., Guvench, O. and MacKerell, Jr., A.D., “Reproducing Crystal Binding Modes of Ligand Functional Groups using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations,” Journal of Chemical Information and Modeling, 51, 877-890, 2011, PMC309022