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Phillip Hudson
Phillip Hudson
Pfizer
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Title
Cited by
Cited by
Year
Multiscale free energy simulations: An efficient method for connecting classical MD simulations to QM or QM/MM free energies using non-Boltzmann Bennett reweighting schemes
G König, PS Hudson, S Boresch, HL Woodcock
Journal of chemical theory and computation 10 (4), 1406-1419, 2014
1312014
Use of nonequilibrium work methods to compute free energy differences between molecular mechanical and quantum mechanical representations of molecular systems
PS Hudson, HL Woodcock, S Boresch
The Journal of Physical Chemistry Letters 6 (23), 4850-4856, 2015
672015
Accelerating QM/MM free energy computations via intramolecular force matching
PS Hudson, S Boresch, DM Rogers, HL Woodcock
Journal of chemical theory and computation 14 (12), 6327-6335, 2018
492018
Origins of the mechanochemical coupling of peptide bond formation to protein synthesis
B Fritch, A Kosolapov, P Hudson, DA Nissley, HL Woodcock, C Deutsch, ...
Journal of the American Chemical Society 140 (15), 5077-5087, 2018
352018
Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities
FL Kearns, PS Hudson, HL Woodcock, S Boresch
Journal of Computational Chemistry 38 (16), 1376-1388, 2017
352017
Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes
PS Hudson, JK White, FL Kearns, M Hodoscek, S Boresch, HL Woodcock
Biochimica et Biophysica Acta (BBA)-General Subjects 1850 (5), 944-953, 2015
322015
Use of interaction energies in QM/MM free energy simulations
PS Hudson, HL Woodcock, S Boresch
Journal of chemical theory and computation 15 (8), 4632-4645, 2019
262019
Force matching as a stepping stone to QM/MM CB [8] host/guest binding free energies: a SAMPL6 cautionary tale
PS Hudson, K Han, HL Woodcock, BR Brooks
Journal of computer-aided molecular design 32 (10), 983-999, 2018
252018
Prediction of CB [8] host–guest binding free energies in SAMPL6 using the double-decoupling method
K Han, PS Hudson, MR Jones, N Nishikawa, F Tofoleanu, BR Brooks
Journal of computer-aided molecular design 32 (10), 1059-1073, 2018
162018
A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge
M Ghorbani, PS Hudson, MR Jones, F Aviat, R Meana-Pañeda, ...
Journal of computer-aided molecular design 35 (5), 667-677, 2021
72021
Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge
A Krämer, PS Hudson, MR Jones, BR Brooks
Journal of computer-aided molecular design 34, 471-483, 2020
72020
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches
PS Hudson, F Aviat, R Meana-Pañeda, L Warrensford, BC Pollard, ...
Journal of Computer-Aided Molecular Design 36 (4), 263-277, 2022
62022
Enantiomerization of Axially Chiral Biphenyls: Polarizable MD Simulations in Water and Butylmethylether
V Zeindlhofer, P Hudson, ÁM Pálvölgyi, M Welsch, M Almarashi, ...
International Journal of Molecular Sciences 21 (17), 6222, 2020
52020
Hierarchical Markov state model building to describe molecular processes
DK Wolfe, JR Persichetti, AK Sharma, PS Hudson, HL Woodcock, ...
Journal of chemical theory and computation 16 (3), 1816-1826, 2020
52020
Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis
FL Kearns, PS Hudson, S Boresch, HL Woodcock
Methods in Enzymology 577, 75-104, 2016
52016
Modeling Ensembles of Enzyme Reaction Pathways with Hi-MSM Reveals the Importance of Accounting for Pathway Diversity
JR Persichetti, Y Jiang, PS Hudson, EP O’Brien
The Journal of Physical Chemistry B 126 (47), 9748-9758, 2022
2022
Failure of the interaction energy approximation
P Hudson, HL Woodcock, S Boresch
American Chemical Society SciMeetings 1 (1), 2020
2020
Breakthroughs in Obtaining QM/MM Free Energies
PS Hudson
University of South Florida, 2020
2020
Mechanistic Understanding of the Thermal and Barrier Properties of PET and PEF Via Computation
BC Knott, G Schmidt, P Hudson, G Beckham, HL Woodcock, MF Crowley, ...
2018 AIChE Annual Meeting, 2018
2018
How Mechanical Forces on the Ribosome Modulate the Speed of Protein Synthesis
B Fritch, S Leininger, P Hudson, L Woodcock, C Deutsch, EP O'Brien
Biophysical Journal 114 (3), 593a, 2018
2018
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Articles 1–20