Jonathon B Ferrell
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Explore the profile of Jonathon B Ferrell including associated specialties, affiliations and a list of published articles.
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9
Citations
58
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Recent Articles
1.
McCarthy D, Remington J, Ferrell J, Schneebeli S, Li J
J Chem Theory Comput
. 2023 Oct;
19(21):7873-7881.
PMID: 37877553
DNA nanostructures have emerged as promising nanomedical tools due to their biocompatibility and tunable behavior. Recent work has shown that DNA nanocages decorated with organic dendrimers strongly bind human serum...
2.
Remington J, McKay K, Beckage N, Ferrell J, Schneebeli S, Li J
J Comput Aided Mol Des
. 2023 Feb;
37(3):147-156.
PMID: 36840893
Molecules with bioactivity towards G protein-coupled receptors represent a subset of the vast space of small drug-like molecules. Here, we compare machine learning models, including dilated graph convolutional networks, that...
3.
Remington J, Ferrell J, Schneebeli S, Li J
J Chem Theory Comput
. 2022 May;
18(6):3921-3929.
PMID: 35507824
Peptide binding to membranes is common and fundamental in biochemistry and biophysics and critical for applications ranging from drug delivery to the treatment of bacterial infections. However, it is largely...
4.
Machine Learning in a Molecular Modeling Course for Chemistry, Biochemistry, and Biophysics Students
Remington J, Ferrell J, Zorman M, Petrucci A, Schneebeli S, Li J
Biophysicist (Rockv)
. 2021 Aug;
1(2).
PMID: 34337350
Recent advances in computer hardware and software, particularly the availability of machine learning libraries, allow the introduction of data-based topics such as machine learning into the Biophysical curriculum for undergraduate...
5.
Remington J, McKay K, Ferrell J, Schneebeli S, Li J
Biophys J
. 2021 Jun;
120(14):2848-2858.
PMID: 34087207
Large-scale conformational transitions in the spike protein S2 domain are required during host-cell infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although conventional molecular dynamics simulations have...
6.
Van Oort C, Ferrell J, Remington J, Wshah S, Li J
J Chem Inf Model
. 2021 Mar;
61(5):2198-2207.
PMID: 33787250
Antibiotic resistance is a critical public health problem. Each year ∼2.8 million resistant infections lead to more than 35 000 deaths in the U.S. alone. Antimicrobial peptides (AMPs) show promise...
7.
Remington J, Liao C, Sharafi M, Ste Marie E, Ferrell J, Hondal R, et al.
J Phys Chem Lett
. 2020 Oct;
11(21):9501-9506.
PMID: 33108730
By integrating various simulation and experimental techniques, we discovered that antimicrobial peptides (AMPs) may achieve synergy at an optimal concentration and ratio, which can be caused by aggregation of the...
8.
Rajappan S, McCarthy D, Campbell J, Ferrell J, Sharafi M, Ambrozaite O, et al.
Angew Chem Int Ed Engl
. 2020 Jun;
59(38):16668-16674.
PMID: 32525593
Selective monofunctionalization of substrates with distant, yet equally reactive functional groups is difficult to achieve, as it requires the second functional group to selectively modulate its reactivity once the first...
9.
Zhao X, Liao C, Ma Y, Ferrell J, Schneebeli S, Li J
J Chem Theory Comput
. 2019 Jan;
15(3):1514-1522.
PMID: 30677300
Modeling peptide assembly from monomers on large time and length scales is often intractable at the atomistic resolution. To address this challenge, we present a new approach which integrates coarse-grained...