Below are selected publications from all recent years; please check here to cite the use of QSite

• •  Hanoian, P.; Hammes-Schiffer S., "Water in the active site of ketosteroid isomerase," Biochemistry., 2011, 50, 6689-6700
• •  Du, J.; Sun, H.; Xi, L.; Li, J.; Yang, Y.; Liu, H.; Yao, X., "Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and Prime/MM-GBSA calculation," J. Comp. Chem., 2011, 32(13), 2800-2809
• •  Bochevarov, A.D.; Li, J.; Song, W.J.; Friesner, R.A.; Lippard, S.J., "Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases," J. Am. Chem. Soc., 2011, 133, 7384-97
• •  Amara, P.; Mouesca, J. M.; Volbeda, A.; Fontecilla-Camps, J.C., "Carbon Monoxide Dehydrogenase Reaction Mechanism: A Likely Case of Abnormal CO2 Insertion to a Ni-H^- Bond," Inorg. Chem., 2011, 50, 1868-1878
• •  Pipirou Z., Guallar V., Basran J., Metcalfe C.L., Murphy E.J., Bottrill A.R., Mistry S.C., Raven E.L., "Peroxide-dependent formation of a covalent link between Trp51 and the heme in cytochrome c peroxidase," Biochemistry, 2009, 48, 3593-3599
• •  ö  Tian L., Friesner R.A., "QM/MM simulation on P450 BM3 enzyme catalysis mechanism," J. Chem. Theory Comput., 2009, 5, 1421-1431
• •  Nicolet, Y.; Amara, P.; Mouesca, J. M.; Fontecilla-Camps, J.C., "Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins," Proc Natl Acad Sci USA, 2009, 106, 14867-14871
• •  Swiderek K., Panczakiewicz A., Bujacz A., Bujacz G., Paneth P., "Modeling of isotope effects on binding oxamate to lactic dehydrogenase," J. Phys. Chem. B, 2009, 113, 12782-12789
• •  Bembenek, S.D.; Keith, J.M.; Letavic, M.A.; Apodaca, R.; Barbier, A.J.; Dvorak, L.; Aluisio, L.; Miller, K.L.; Lovenberg, T.W.; Carruthers, N.I., "Lead identification of acetylcholinesterase inhibitors–histamine H₃ receptor antagonists from molecular modeling," Bioorg. & Med. Chem., 2008, 16, 2968-2973
• •  Fischmann, T.O.; Hruza, A.; Duca, J.S.; Ramanathan, L.; Mayhood, T.; Windsor, W.T.; Le, H.V.; Guzi, T.J.; Dwyer, M.P.; Paruch, K.; Doll, R.J.; Lees, E.; Parry, D.; Seghezzi, W.; Madison, V., "Structure-guided discovery of cyclin-dependent kinase inhibitors," Biopolymers, 2008, 89, 372-379
• •  Rinaldo, D.; Philipp, D.M.; Lippard, S.J.; & Friesner, R.A., "Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study," J. Am. Chem. Soc., 2007, 129, 3135-3147
• •  Guallar, V.; Jarzecki, A.A.; Friesner, R.A.; & Spiro, T.G., "Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery," J. Am. Chem. Soc., 2006, 128, 5427-5435
• •  Gherman, B. F.; Lippard, S. J.; Friesner R. A., "Substrate hydroxylation in methane monooxygenase: Quantitative modeling via mixed quantum mechanics/molecular mechanics techniques," J. Am. Chem. Soc., 2005, 127, 1025-1037
• •  ö  Guallar, V.; Jacobson, M. P.; McDermott, A.; Friesner, R. A., "Computational Modeling of the Catalytic Reaction in Triosephosphate Isomerase," J. Mol. Biol., 2004, 337, 227-239
• •  Gherman, B. F.; Baik, M.; Lippard, S. J.; Friesner, R. A., "Dioxygen Activation in Methane Monooxygenase: A Theoretical Study," J. Am. Chem. Soc., 2004, 126, 2978-2990
• •  Guallar, V.; Friesner, R. A., "Cytochrome P450CAM Enzymatic Catalysis Cycle: A Quantum Mechanics/Molecular Mechanics Study," J. Am. Chem. Soc. , 2004, 126, 8501-8508
• •  Gherman, B.F.; Goldberg, S. D.; Cornish, V. W.; Friesner, R. A., "Mixed Quantum Mechanical/ Molecular Mechanical (QM/MM) Study of the Deacylation Reaction in a Penicillin Binding Protein (PBP) Versus in a Class C β-Lactamase ," J. Am. Chem. Soc. , 2004, 126, 7652-7664
• •  Baik, M.; Friesner, R. A.; Lippard, S. J., "Theoretical Study of Cisplatin Binding to Purine Bases: Why Does Cisplatin Prefer Guanine over Adenine as Substrate?," J. Am. Chem. Soc., 2003, 125, 14082-14092
• •  Baik, M.; Newcomb, M.; Friesner, R. A.; Lippard, S. J., "Mechanistic Studies on the Hydroxylation of Methane by Methane Monooxygenase," Chemical Reviews, 2003, 103, 2385-2419
• •  Guallar, V.; Baik, M.; Lippard, S. J.; Friesner, R. A., "Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450," Proc. Nat. Acad. Sci. USA, 2003, 100, 6998-7002
• •  Friesner, R. A.; Baik, M.; Guallar, V.; Gherman, B. F.; Wirstam, M.; Murphy, R. B.; Lippard, S. J., "How iron-containing proteins control dioxygen chemistry: a detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations," Coordination Chemistry Reviews, 2003, 238-239, 267-290
• •  Wirstam, M; Lippard, S.J.; Friesner, R.A., "Reversible dioxygen binding to hemerythrin," J. Am. Chem. Soc. , 2003, 125, 3980-3987
• •  Baik, M.; Gherman, B. F.; Friesner, R. A., Lippard, S. J., "Hydroxylation of Methane by Non-Heme Diiron Enzymes: Molecular Orbital Analysis of the C-H Bond Activation by Reactive Intermediate Q," J. Am. Chem. Soc., 2002, 124, 14608-14615
• •  Murphy, R. B.; Philipp, D. M.; Friesner, R. A., "A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments," J. Comp. Chem., 2000, 21, 1442-1457
• •  Philipp, D. M.; Friesner, R. A., "Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide," J. Comp. Chem., 1999, 20, 1468-1494

• ö indicates papers (co)authored by Schrödinger scientist(s).