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Pengfei Li
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AMBER 2021
A Onufriev, F Pan, S Pantano, R Qi, A Rahnamoun, DR Roe, A Roitberg, ...
University of California: San Francisco, 2021
5471*2021
Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent
P Li, BP Roberts, DK Chakravorty, KM Merz Jr
Journal of Chemical Theory and Computation 9 (6), 2733-2748, 2013
6842013
MCPB.py: A python based metal center parameter builder
P Li, KM Merz Jr
Journal of chemical information and modeling 56 (4), 599-604, 2016
5152016
Systematic parameterization of monovalent ions employing the nonbonded model
P Li, LF Song, KM Merz Jr
Journal of chemical theory and computation 11 (4), 1645-1657, 2015
3762015
Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions
P Li, KM Merz Jr
Journal of Chemical Theory and Computation 10 (1), 289-297, 2014
3682014
Metal ion modeling using classical mechanics
P Li, KM Merz Jr
Chemical reviews 117 (3), 1564-1686, 2017
3272017
Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water
P Li, LF Song, KM Merz Jr
The Journal of Physical Chemistry B 119 (3), 883-895, 2014
3022014
AMBER 2018
TA Darden, RE Duke, D Ghoreishi, MK Gilson, H Gohlke, AW Goetz, ...
University of California, San Francisco, 2018
232*2018
AmberTools
DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ...
Journal of Chemical Information and Modeling, 2023
2172023
AMBER 2015
DA Case, J Berryman, RM Betz, DS Cerutti, TE Cheatham Iii, TA Darden, ...
University of California, 2015
171*2015
QM/MM studies into the H2O2-dependent activity of lytic polysaccharide monooxygenases: evidence for the formation of a caged hydroxyl radical intermediate
B Wang, EM Johnston, P Li, S Shaik, GJ Davies, PH Walton, C Rovira
ACS Catalysis 8 (2), 1346-1351, 2018
1372018
AMBER 2016
DS Cerutti, TE Cheatham III, TA Darden, RE Duke, TJ Giese, H Gohlke, ...
University of California, San Francisco, 2016
128*2016
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models
A Sengupta, Z Li, LF Song, P Li, KM Merz Jr
Journal of Chemical Information and Modeling, 2021
1112021
Systematic Parameterization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models
Z Li, LF Song, P Li, KM Merz
Journal of Chemical Theory and Computation, 2020
812020
AMBER 2020
TA Darden, RE Duke, G Giambasu, MK Gilson, H Gohlke, AW Goetz, ...
University of California, San Francisco, 2020
60*2020
Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations
P Li, AV Soudackov, S Hammes-Schiffer
Journal of the American Chemical Society 140 (8), 3068-3076, 2018
522018
Extended Zinc AMBER Force Field (EZAFF)
Z Yu, P Li, KM Merz Jr
Journal of chemical theory and computation 14 (1), 242-254, 2017
512017
Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models
Z Li, LF Song, P Li, KM Merz Jr
Journal of Chemical Theory and Computation, 2021
392021
Formation of an unusual glutamine tautomer in a blue light using flavin photocycle characterizes the light-adapted state
JJ Goings, P Li, Q Zhu, S Hammes-Schiffer
Proceedings of the National Academy of Sciences, 2020
372020
Vibrational signatures of isomeric lithiated N-acetyl-d-hexosamines by Gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy
Y Tan, N Zhao, J Liu, P Li, CN Stedwell, L Yu, NC Polfer
Journal of The American Society for Mass Spectrometry 28 (3), 539-550, 2017
372017
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Articles 1–20