Debsindhu Bhowmik
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Explore the profile of Debsindhu Bhowmik including associated specialties, affiliations and a list of published articles.
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Recent Articles
1.
Bhowmik D, Zhang P, Fox Z, Irle S, Gounley J
Patterns (N Y)
. 2024 Apr;
5(4):100947.
PMID: 38645768
This study examines the effectiveness of generative models in drug discovery, material science, and polymer science, aiming to overcome constraints associated with traditional inverse design methods relying on heuristic rules....
2.
Blanchard A, Gounley J, Bhowmik D, Chandra Shekar M, Lyngaas I, Gao S, et al.
Int J High Perform Comput Appl
. 2024 Apr;
36(5-6):587-602.
PMID: 38603308
The COVID-19 pandemic highlights the need for computational tools to automate and accelerate drug design for novel protein targets. We leverage deep learning language models to generate and score drug...
3.
Zhang P, Kearney L, Bhowmik D, Fox Z, Naskar A, Gounley J
J Chem Inf Model
. 2023 Dec;
63(24):7689-7698.
PMID: 38055952
Transformer-based large language models have remarkable potential to accelerate design optimization for applications such as drug development and material discovery. Self-supervised pretraining of transformer models requires large-scale data sets, which...
4.
Yoo P, Bhowmik D, Mehta K, Zhang P, Liu F, Lupo Pasini M, et al.
Sci Rep
. 2023 Nov;
13(1):20031.
PMID: 37973879
The inverse design of novel molecules with a desirable optoelectronic property requires consideration of the vast chemical spaces associated with varying chemical composition and molecular size. First principles-based property predictions...
5.
Chen S, Weiss K, Stanley C, Bhowmik D
Protein Sci
. 2023 Aug;
32(10):e4772.
PMID: 37646172
Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure-function relationships. Due to the different neutron scattering lengths of hydrogen...
6.
Blanchard A, Bhowmik D, Fox Z, Gounley J, Glaser J, Akpa B, et al.
J Cheminform
. 2023 Jun;
15(1):59.
PMID: 37291633
The vast size of chemical space necessitates computational approaches to automate and accelerate the design of molecular sequences to guide experimental efforts for drug discovery. Genetic algorithms provide a useful...
7.
Zhao Z, Shen X, Chen S, Gu J, Wang H, Mojica M, et al.
Elife
. 2023 Feb;
12.
PMID: 36826989
β-Lactam antibiotics are the most important and widely used antibacterial agents across the world. However, the widespread dissemination of β-lactamases among pathogenic bacteria limits the efficacy of β-lactam antibiotics. This...
8.
Chen S, Londono-Larrea P, McGough A, Bible A, Gunaratne C, Araujo-Granda P, et al.
Front Microbiol
. 2021 Oct;
12:726409.
PMID: 34630352
Agent-based modeling (ABM) is a powerful simulation technique which describes a complex dynamic system based on its interacting constituent entities. While the flexibility of ABM enables broad application, the complexity...
9.
Olehnovics E, Yin J, Perez A, De Fabritiis G, Bonomo R, Bhowmik D, et al.
Front Microbiol
. 2021 Oct;
12:720991.
PMID: 34621251
Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution...
10.
Bux K, Shen X, Tariq M, Yin J, Moin S, Bhowmik D, et al.
Front Mol Biosci
. 2021 Oct;
8:710623.
PMID: 34604302
Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a...