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Debsindhu Bhowmik
Debsindhu Bhowmik
Computational Scientist, Oak Ridge National Laboratory
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ProtTrans: Toward understanding the language of life through self-supervised learning
A Elnaggar, M Heinzinger, C Dallago, G Rehawi, Y Wang, L Jones, ...
IEEE Transactions on Pattern Analysis & Machine Intelligence 44 (10), 7112-7127, 2022
10402022
Supercomputer-based ensemble docking drug discovery pipeline with application to COVID-19
A Acharya, R Agarwal, MB Baker, J Baudry, D Bhowmik, S Boehm, ...
Journal of chemical information and modeling 60 (12), 5832-5852, 2020
1562020
ProtTrans: Towards cracking the language of Life¡¯s code through self-supervised deep learning and high performance computing. arXiv 2020
A Elnaggar, M Heinzinger, C Dallago, G Rihawi, Y Wang, L Jones, ...
arXiv preprint arXiv:2007.06225, 2007
852007
Deep clustering of protein folding simulations
D Bhowmik, S Gao, MT Young, A Ramanathan
BMC bioinformatics 19, 47-58, 2018
762018
Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning
R Romero, A Ramanathan, T Yuen, D Bhowmik, M Mathew, LB Munshi, ...
Proceedings of the National Academy of Sciences 116 (11), 5086-5095, 2019
602019
Aqueous solutions of tetraalkylammonium halides: ion hydration, dynamics and ion-ion interactions in light of steric effects
D Bhowmik, N Malikova, O Bernard, J Teixeira, P Turq
Physical Chemistry Chemical Physics 16 (26), 13447-13457, 2014
572014
Deepdrivemd: Deep-learning driven adaptive molecular simulations for protein folding
H Lee, M Turilli, S Jha, D Bhowmik, H Ma, A Ramanathan
2019 IEEE/ACM Third Workshop on Deep Learning on Supercomputers (DLS), 12-19, 2019
542019
Single chain dynamic structure factor of linear polymers in an all-polymer nano-composite
A Arbe, JA Pomposo, I Asenjo-Sanz, D Bhowmik, O Ivanova, ...
Macromolecules 49 (6), 2354-2364, 2016
472016
Sex disparities and neutralizing-antibody durability to SARS-CoV-2 infection in convalescent individuals
AJ Markmann, N Giallourou, DR Bhowmik, YJ Hou, A Lerner, DR Martinez, ...
Msphere 6 (4), 10.1128/msphere. 00275-21, 2021
452021
Using GANs with adaptive training data to search for new molecules
AE Blanchard, C Stanley, D Bhowmik
Journal of cheminformatics 13, 1-8, 2021
412021
Microscopic dynamics in nanocomposites of poly (ethylene oxide) and poly (methyl methacrylate) soft nanoparticles: A quasi-elastic neutron scattering study
D Bhowmik, JA Pomposo, F Juranyi, V García-Sakai, M Zamponi, Y Su, ...
Macromolecules 47 (1), 304-315, 2014
402014
Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane
QN Van, CA López, M Tonelli, T Taylor, B Niu, CB Stanley, D Bhowmik, ...
Proceedings of the National Academy of Sciences 117 (39), 24258-24268, 2020
392020
Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer
M Sherekar, SW Han, R Ghirlando, S Messing, M Drew, D Rabara, ...
Journal of Biological Chemistry 295 (4), 1105-1119, 2020
392020
Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile
UR Shrestha, D Bhowmik, JRD Copley, M Tyagi, JB Leão, X Chu
Proceedings of the National Academy of Sciences 112 (45), 13886-13891, 2015
362015
Aqueous solutions of ionenes: interactions and counterion specific effects as seen by neutron scattering
N Malikova, S Čebašek, V Glenisson, D Bhowmik, G Carrot, V Vlachy
Physical Chemistry Chemical Physics 14 (37), 12898-12904, 2012
362012
Dynamic Profiling of ¥â-Coronavirus 3CL Mpro Protease Ligand-Binding Sites
E Cho, M Rosa, R Anjum, S Mehmood, M Soban, M Mujtaba, K Bux, ...
Journal of Chemical Information and Modeling 61 (6), 3058-3073, 2021
352021
Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana glycosyltransferases
A Akere, SH Chen, X Liu, Y Chen, SC Dantu, A Pandini, D Bhowmik, ...
Biochemical Journal 477 (15), 2791-2805, 2020
322020
Investigation of a nanocomposite of 75 wt% poly (methyl methacrylate) nanoparticles with 25 wt% poly (ethylene oxide) linear chains: a quasielatic neutron scattering ¡¦
D Bhowmik, JA Pomposo, F Juranyi, V García Sakai, M Zamponi, A Arbe, ...
Macromolecules 47 (9), 3005-3016, 2014
272014
Quasi-elastic neutron scattering reveals ligand-induced protein dynamics of a G-protein-coupled receptor
UR Shrestha, SMDC Perera, D Bhowmik, U Chawla, E Mamontov, ...
The journal of physical chemistry letters 7 (20), 4130-4136, 2016
252016
Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study
GK Dhindsa*, D Bhowmik* (*Equal Contribution), M Goswami, HM O'Neill, ...
The Journal of Physical Chemistry B, 2016
242016
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