Phillip S Hudson
Overview
Explore the profile of Phillip S Hudson including associated specialties, affiliations and a list of published articles.
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Articles
15
Citations
213
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Recent Articles
1.
Hwang W, Austin S, Blondel A, Boittier E, Boresch S, Buck M, et al.
J Phys Chem B
. 2024 Sep;
128(41):9976-10042.
PMID: 39303207
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in...
2.
Smith A, Plazola M, Hudson P, Tapavicza E
J Phys Chem B
. 2024 Sep;
128(37):8956-8965.
PMID: 39240094
Photoinduced vitamin D formation occurs 10-15-fold faster in phospholipid bilayers (PLB) than in isotropic solution. It has been hypothesized that amphipatic interactions of the PLB with the rotationally flexible previtamin...
3.
Persichetti J, Jiang Y, Hudson P, OBrien E
J Phys Chem B
. 2022 Nov;
126(47):9748-9758.
PMID: 36383711
Conventional quantum mechanical-molecular mechanics (QM/MM) simulation approaches for modeling enzyme reactions often assume that there is one dominant reaction pathway and that this pathway can be sampled starting from an...
4.
Hudson P, Aviat F, Meana-Paneda R, Warrensford L, Pollard B, Prasad S, et al.
J Comput Aided Mol Des
. 2022 May;
36(4):263-277.
PMID: 35597880
Accurately predicting free energy differences is essential in realizing the full potential of rational drug design. Unfortunately, high levels of accuracy often require computationally expensive QM/MM Hamiltonians. Fortuitously, the cost...
5.
Ghorbani M, Hudson P, Jones M, Aviat F, Meana-Paneda R, Klauda J, et al.
J Comput Aided Mol Des
. 2021 May;
35(5):667-677.
PMID: 33939083
In this study, we report binding free energy calculations of various drugs-of-abuse to Cucurbit-[8]-uril as part of the SAMPL8 blind challenge. Force-field parameters were obtained from force-matching with different quantum...
6.
Kramer A, Hudson P, Jones M, Brooks B
J Comput Aided Mol Des
. 2020 Feb;
34(5):471-483.
PMID: 32060677
Accurately computing partition coefficients is a pivotal part of drug discovery. Specifically, octanol-water partition coefficients can provide information into hydrophobicity of drug-like molecules, as well as a de facto representation...
7.
Wolfe D, Persichetti J, Sharma A, Hudson P, Woodcock H, OBrien E
J Chem Theory Comput
. 2020 Feb;
16(3):1816-1826.
PMID: 32011146
Markov state models can describe ensembles of pathways via kinetic networks but are difficult to create when large free-energy barriers limit unbiased sampling. Chain-of-states simulations allow sampling over large free-energy...
8.
Hudson P, Woodcock H, Boresch S
J Chem Theory Comput
. 2019 May;
15(8):4632-4645.
PMID: 31142113
The use of the most accurate (i.e., QM or QM/MM) levels of theory for free energy simulations (FES) is typically not possible. Primarily, this is because the computational cost associated...
9.
Hudson P, Boresch S, Rogers D, Woodcock H
J Chem Theory Comput
. 2018 Oct;
14(12):6327-6335.
PMID: 30300543
The calculation of free energy differences between levels of theory has numerous potential pitfalls. Chief among them is the lack of overlap, i.e., ensembles generated at one level of theory...
10.
Hudson P, Han K, Woodcock H, Brooks B
J Comput Aided Mol Des
. 2018 Oct;
32(10):983-999.
PMID: 30276502
Use of quantum mechanical/molecular mechanical (QM/MM) methods in binding free energy calculations, particularly in the SAMPL challenge, often fail to achieve improvement over standard additive (MM) force fields. Frequently, the...