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 | 132 | 2014 |
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 | 69 | 2015 |
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 | 49 | 2018 |
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 | 36 | 2018 |
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 | 35 | 2017 |
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 | 32 | 2015 |
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 | 26 | 2019 |
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 | 25 | 2018 |
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 | 16 | 2018 |
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 | 7 | 2021 |
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 | 7 | 2020 |
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 | 6 | 2022 |
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 | 6 | 2020 |
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 | 6 | 2016 |
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 | 5 | 2020 |
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 |