Publications
(* represents corresponding authors)
Publication list via Google Scholar
Publications after joining Loyola
Journal Articles
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L. Dong, P. Li, B. Wang,* “Enhancing MM/P(G)BSA Methods: Integration of Formulaic Entropy for Improved Binding Free Energy Calculations and Virtual Screening Efficiency”, Submitted, preprint available at ChemRxiv, DOI: 10.26434/chemrxiv-2024-9308m
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F. Hu, Y. Zhang, P. Li, R. Wu, and F. Xia.* “Development of Accurate Force Fields for Mg2+ and Triphosphate Interactions in ATP∙Mg2+ and GTP∙Mg2+ Complexes”, J. Chem. Theory Comput, 2024, Article ASAP, DOI: 10.1021/acs.jctc.4c01142
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B. Hanson, M. Smith, and P. Li,* “Accuracy of Discrete-Continuum Solvation Model for Cations: A Benchmark Study”, J. Phys. Chem. B, 2024, Article ASAP, DOI: 10.1021/acs.jpcb.4c04034
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L. Landry and P. Li,* “Parameterization of a Fluctuating Charge Model for Complexes Containing 3d Transition Metals”, J. Phys. Chem. B, 2024, Article ASAP, DOI: 10.1021/acs.jpcb.4c03219
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M. Smith, R. Khatiwada, and P. Li,* “Exploring Ion Polarizabilities and Their Correlation with van der Waals Radii: A Theoretical Investigation”, J. Chem. Theory Comput, 2024, Article ASAP, DOI: 10.1021/acs.jctc.4c00632
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Z. Li, S. Bhowmik, L. Sagresti, G. Brancato, M. Smith, D. E. Benson, P. Li, and K. M. Merz Jr.,* “Simulating Metal-Imidazole Complexes”, J. Chem. Theory Comput, 2024, 20, 6706-6716.
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Y. Wei, P. Li,* “Theoretical Insights into the Reduction of Azurin Metal Site with Unnatural Amino Acid Substitutions”, J. Inorg. Biochem., 2024, 259, 112651.
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D. Fang, Z. Zhang, J. Zhai, B. Guo, P. Li, X. Liu, J. Song, S. Xie, R. Wu, Y. Zhao,* C. Wang,* “Enzymatic-related network of catalysis, polyamine, and tumors for acetylpolyamine oxidase: from calculation to experiment”, Chem. Sci., 2024, 15, 2867-2882.
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L. Landry, P. Li,* “Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins”, J. Chem. Inf. Model.,, 2024, 64, 812-824.
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D. Case, H. Aktulga, K. Belfon, D. Cerutti, G. Cisneros, V. Cruzeiro, N. Forouzesh, T. Giese, A. Götz, H. Gohlke, S. Izadi, K. Kasavajhala, M. Kaymak, E. King, T. Kurtzman, T. Lee, P. Li, J. Liu, T. Luchko, R. Luo, M. Machado, M. Manathunga, H. Nguyen, K. O'Hearn, A. Onufriev, F. PAN, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T. Cheatham, D. Roe, A. Roitberg, C. Simmerling, D. York, M. Nagan,* and K. Merz,* “AmberTools”, J. Chem. Inf. Model., 2023, 63, 6183-6191.
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X. Yang, S. Liu, Z. Yin, M. Chen, J. Song, P. Li, and L. Yang,* “New insight into the proton pumping mechanism of ba3 Cytochrome c Oxidase: the functions of key residues and waters”, Phys. Chem. Chem. Phys. 2023, 25, 25105-25115.
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A. Sharma, C. Whittington, M. Jabed, S. G. Hill, A. Kostenko, T. Yu, P. Li, P. E. Doan, B. M. Hoffman,* and A. R. Offenbacher,* “13C Electron Nuclear Double Resonance Spectroscopy-Guided Molecular Dynamics Computations Reveal the Structure of the Enzyme-Substrate Complex of an Active, N-linked Glycosylated Lipoxygenase”, Biochemistry, 2023, 62, 1531-1543.
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M. Smith, Z. Li, L. Landry, K. M. Merz, Jr.,* and P. Li,* “Consequences of Overfitting the van der Waals Radii of Ions”, J. Chem. Theory Comput, 2023, Article ASAP, DOI: 10.1021/acs.jctc.2c01255
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W. Fang, S. Feng, Z. Jiang, W. Liang, P. Li,* and B. Wang,* “Understanding the Key Roles of pH Buffer in Accelerating the Lignin Degradation by Lignin Peroxidases”, JACS Au, 2023, 3, 536-549.
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T. Gerard, Y. Wei, E. Weerawardhana, A. Lugosan, M. Zeller, D. Dickie, P. Li,* and W. T. Lee,* “Novel Inorganic Fluorescent Chemosensor: Rational Design and Selective Mg2+ Detection”, ACS Omega, 2023, 8, 3835-3841.
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M. Smith and P. Li,* “Molecular Insights into the Calcium Binding in Troponin C Through a Molecular Dynamics Study”, J. Chem. Inf. Model., 2023, 63, 354-361.
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A. J. Veenis, P. Li, A. V. Soudackov, S. Hammes-Schiffer, and P. C. Bevilacqua,* “Investigation of the pKa of the Nucleophilic O2′ of the Hairpin Ribozyme”, J. Phys. Chem. B., 2021, 125, 11869.
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P. Li,* “Bridging the 12-6-4 Model and the Fluctuating Charge Model”, Front. Chem., 2021, 9:721960.
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Z. Li, L. F. Song, P. Li,* and K. M. Merz, Jr.,* “Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models”, J. Chem. Theory Comput., 2021, 17, 2342-2354.
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A. Sengupta, Z. Li, L. F. Song, P. Li,* and K. M. Merz. Jr.* “Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models”, J. Chem. Inf. Model.., 2021, 61, 869-880. (A correction published at J. Chem. Inf. Model., 2021, 61, 3734-3735.
Book Chapters
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Yang Wei and P. Li,* “Modeling Metal Ions in Enzyme Catalysis”, Compr. Comput. Chem. 2022, In print, DOI: 10.1016/B978-0-12-821978-2.00019-2
Software Packages (Dr. Li has been an AMBER developer since 2015)
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D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, N. Forouzesh, G. Giamba¸su, T. Giese, M.K. Gilson, H. Gohlke, A.W. Goetz, J. Harris, Z. Huang, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, A. Kovalenko, T. Kurtzman, T.S. Lee, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, X. Wu, Y. Wu, Y. Xiong, Y. Xue, D.M. York, C. Zhao, Q. Zhu, and P.A. Kollman (2024), Amber 2024, University of California, San Francisco.
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D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, N. Forouzesh, G. Giamba¸su, T. Giese, M.K. Gilson, H. Gohlke, A.W. Goetz, J. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, H. Wei, X. Wu, Y. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, Q. Zhu, and P.A. Kollman (2023), Amber 2023, University of California, San Francisco.
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D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022, University of California, San Francisco.
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D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, C. Jin, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2021), AMBER 2021, University of California, San Francisco.
Publications before joining Loyola
Journal Articles
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J. J. Goings, P. Li, Q. Zhu, and S. Hammes-Schiffer,* “Formation of an Unusual Glutamine Tautomer in a Blue-Light Using Flavin Photocycle Characterizes the Light-Adapted State”, Proc. Natl. Acad. Sci. U. S. A., 2020, 117, 26626-26632.
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P. Li, A. V. Soudackov, B. Koronkiewicz, J. M. Mayer, and S. Hammes-Schiffer,* “Theoretical Study of Shallow Distance Dependence of Proton-Coupled Electron Transfer in Oligoproline Peptides”, J. Am. Chem. Soc. 2020, 142, 13795-13804.
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C. R. Reinhardt, P. Li, G. Kang, J. Stubbe, C. L. Drennan, and S. Hammes-Schiffer,* “Conformational Motions and Water Networks at the 𝛼/𝛽 Interface in E. coli Ribonucleotide Reductase”, J. Am. Chem. Soc. 2020, 142, 13768-13778.
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Z. Li, L. F. Song, P. Li,* and K. M. Merz, Jr.,* “Systematic Parameterization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models”, J. Chem. Theory Comput., 2020, 16, 4429-4442.
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P. Li, A. Rangadurai, H. M. Al-Hashimi, and S. Hammes-Schiffer,* “Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations”, J. Am. Chem. Soc. 2020, 142, 11183-11191.
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P. Li and S. Hammes-Schiffer,* “Substrate-to-Product Conversion Facilitates Active Site Loop Opening in Yeast Enolase: A Molecular Dynamics Study”, ACS Catal. 2019, 9, 8985-8990.
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P. Li, A. V. Soudackov and S. Hammes-Schiffer,* “Impact of Mutations on the Binding Pocket of Soybean Lipoxygenase: Implications for Proton-Coupled Electron Transfer”, J. Phys. Chem. Lett. 2018, 9, 6444-6449.
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P. Li, A. V. Soudackov and S. Hammes-Schiffer,* “Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations”, J. Am. Chem. Soc. 2018, 140, 3068-3076.
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B. Wang, E. Johnston, P. Li, S. Shaik, G. Davies, P. H. Walton and C. Rovira,* “QM/MM Studies into the H2O2-Dependent Activity of Lytic Polysaccharide Monooxygenases: Evidence for the Formation of a Caged Hydroxyl Radical Intermediate”, ACS Catal. 2018, 8, 1346-1351.
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Y. Tan, N. Zhao, J. Liu, P. Li, C. N. Stedwell, L. Yu and N. C. Polfer,* “Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy”, J. Am. Soc. Mass Spectrom. 2017, 28, 539-550.
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Z. Yu, P. Li and K. M. Merz, Jr.,* “Extended Zinc AMBER Force Field (EZAFF)”, J. Chem. Theory Comput. 2018, 14, 242-254.
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Z. Yu, P. Li and K. M. Merz, Jr.,* “Using Ligand-Induced Protein Chemical Shift Perturbations to Determine Protein-Ligand Structures”, Biochemistry 2017, 56, 2349-2362.
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P. Li and K. M. Merz, Jr.,* “Metal Ion Modeling Using Classical Mechanics”, Chem. Rev. 2017, 117, 1564-1686.
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P. Li and K. M. Merz, Jr.,* “MCPB.py: A Python Based Metal Center Parameter Builder”, J. Chem. Inf. Model. 2016, 56, 599-604.
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D. K. Chakravorty,* P. Li, T. T. Tran, C. A. Bayse and K. M. Merz, Jr.,* “Metal Ion Capture Mechanism of a Copper Metallochaperone”, Biochemistry 2016, 55, 501-509.
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P. Li, L. F. Song and K. M. Merz, Jr.,* “Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model”, J. Chem. Theory Comput. 2015, 11, 1645-1657.
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Z. Zheng, T. Wang, P. Li and K. M. Merz, Jr.,* “KECSA-Movable Type Implicit Solvation Model (KMTISM)”, J. Chem. Theory Comput. 2015, 11, 667-682.
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P. Li, L. F. Song and K. M. Merz, Jr.,* “Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water”, J. Phys. Chem. B 2015, 119, 883-895.
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P. Li and K. M. Merz, Jr.,* “Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions”, J. Chem. Theory Comput. 2014, 10, 289-297.
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P. Li, B. P. Roberts, D. K. Chakravorty and K. M. Merz, Jr.,* “Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent”, J. Chem. Theory Comput. 2013, 9, 2733-2748.
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M. Lin, P. Li and Z. Cao,* “Effects of Structural Modification on the Ground State of Metallabenzenes: Singlet versus Triplet State”, J. Theor. Comput. Chem. 2011, 10, 861-874.
Book Chapters
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P. Li and K. M. Merz, Jr.,* “Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program”, Methods Mol. Biol. 2021, 2199, 257-275.
Software Packages (Dr. Li has been an AMBER developer since 2015)
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D. A. Case, K. Belfon, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, T. E. Cheatham, III, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, G. Giambasu, M. K. Gilson, H. Gohlke, A. W. Goetz, R Harris, S. Izadi, K. Kasavajhala, A. Kovalenko, R. Krasny, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K. M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F. Pan, S. Pantano, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, N. Skrynnikov, J. Smith, J. Swails, R. C. Walker, J. Wang, L. Wilson, R. M. Wolf, X. Wu, D. M. York and P. A. Kollman (2020), AMBER 2020, University of California, San Francisco.
- D. A. Case, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, T. E. Cheatham, III, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, D. Ghoreishi, G. Giambasu, T. Giese, M. K. Gilson, H. Gohlke, A. W. Goetz, D. Greene, R. Harris, N. Homeyer, Y. Huang, S. Izadi, A. Kovalenko, R. Krasny, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, D. J. Mermelstein, K. M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, A. Onufriev, F. Pan, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, J. Smith, J. Swails, R. C. Walker, J. Wang, H. Wei, L. Wilson, R. M. Wolf, X. Wu, L. Xiao, Y. Xiong, D. M. York and P. A. Kollman (2019), AMBER 2019, University of California, San Francisco.
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D. A. Case, S. R. Brozell, D. S. Cerutti, T. E. Cheatham, III, V. W .D. Cruzeiro, T. A. Darden, R. E. Duke, D. Ghoreishi, H. Gohlke, A. W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A. Kovalenko, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D. J. Mermelstein, K. M. Merz, Y. Miao, G. Monard, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, J. Smith, J. Swails, R. C. Walker, J. Wang, H. Wei, R. M. Wolf, X. Wu, L. Xiao, D. M. York and P. A. Kollman (2018), AMBER 2018, University of California, San Francisco.
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D. A. Case, D. S. Cerutti, T. E. Cheatham, III, T. A. Darden, R. E. Duke, T. J. Giese, H. Gohlke, A. W. Goetz, D. Greene, N. Homeyer, S. Izadi, A. Kovalenko, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D. Mermelstein, K. M. Merz, G. Monard, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, C. L. Simmerling, W. M. Botello-Smith, J. Swails, R. C. Walker, J. Wang, R. M. Wolf, X. Wu, L. Xiao, D. M. York and P. A. Kollman (2017), AMBER 2017, University of California, San Francisco.
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D. A. Case, R. M. Betz, W. Botello-Smith, D. S. Cerutti, T. E. Cheatham, III, T. A. Darden, R. E. Duke, T. J. Giese, H. Gohlke, A. W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T. S. Lee, S. LeGrand, P. Li, C. Lin, T. Luchko, R. Luo, B. Madej, D. Mermelstein, K. M. Merz, G. Monard, H. Nguyen, H. T. Nguyen, I. Omelyan, A. Onufriev, D. R. Roe, A. Roitberg, C. Sagui, C. L. Simmerling, J. Swails, R. C. Walker, J. Wang, R. M. Wolf, X. Wu, L. Xiao, and P. A. Kollman (2016), AMBER 2016, University of California, San Francisco.
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D. A. Case, J. T. Berryman, R. M. Betz, D. S. Cerutti, T. E. Cheatham, III, T. A. Darden, R. E. Duke, T. J. Giese, H. Gohlke, A. W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T. S. Lee, S. LeGrand, P. Li, T. Luchko, R. Luo, B. Madej, K. M. Merz, Jr., G. Monard, P. Needham, H. Nguyen, I. Omelyan, A. Onufriev, D. R. Roe, A. Roitberg, R. Salomon-Ferrer, C. L. Simmerling, W. Smith, J. Swails, R. C. Walker, J. Wang, R. M. Wolf, X. Wu, D. M. York and P. A. Kollman (2015), AMBER 2015, University of California, San Francisco.