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Prabin Baral
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Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B. 1.617. 2 and implications for immune evasion
P Baral, N Bhattarai, ML Hossen, V Stebliankin, BS Gerstman, ...
Biochemical and biophysical research communications 574, 14-19, 2021
802021
Potential autoimmunity resulting from molecular mimicry between SARS-CoV-2 spike and human proteins
J Nunez-Castilla, V Stebliankin, P Baral, CA Balbin, M Sobhan, ...
Viruses 14 (7), 1415, 2022
642022
Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140
R Pokhrel, N Bhattarai, P Baral, BS Gerstman, JH Park, M Handfield, ...
Physical Chemistry Chemical Physics 21 (23), 12530-12539, 2019
372019
Structural and dynamical differences in the spike protein RBD in the SARS-CoV-2 variants B. 1.1. 7 and B. 1.351
N Bhattarai, P Baral, BS Gerstman, PP Chapagain
The Journal of Physical Chemistry B 125 (26), 7101-7107, 2021
362021
Significance of the RBD mutations in the SARS-CoV-2 omicron: from spike opening to antibody escape and cell attachment
ML Hossen, P Baral, T Sharma, B Gerstman, P Chapagain
Physical Chemistry Chemical Physics 24 (16), 9123-9129, 2022
242022
Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus
R Pokhrel, R Shakya, P Baral, P Chapagain
Journal of Chemical Information and Modeling 62 (20), 4955-4962, 2022
172022
In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic fever
P Baral, E Pavadai, BS Gerstman, PP Chapagain
Scientific Reports 10 (1), 7667, 2020
172020
Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes
CA Balbin, J Nunez-Castilla, V Stebliankin, P Baral, M Sobhan, ...
ImmunoInformatics 9, 100023, 2023
112023
Conformational Flexibility of the Protein–Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament
E Pavadai, N Bhattarai, P Baral, RV Stahelin, PP Chapagain, ...
The Journal of Physical Chemistry B 123 (43), 9045-9053, 2019
102019
EMoMiS: A pipeline for epitope-based molecular mimicry search in protein structures with applications to SARS-CoV-2
V Stebliankin, P Baral, C Balbin, J Nunez-Castilla, M Sobhan, T Cickovski, ...
BioRxiv, 2022.02. 05.479274, 2022
72022
Lipid II binding and transmembrane properties of various antimicrobial lanthipeptides
R Pokhrel, N Bhattarai, P Baral, BS Gerstman, JH Park, M Handfield, ...
Journal of Chemical Theory and Computation 18 (1), 516-525, 2021
72021
Structural insights into the repair mechanism of AGT for methyl-induced DNA damage
RP Koirala, R Pokhrel, P Baral, PB Tiwari, PP Chapagain, NP Adhikari
Biological Chemistry 402 (10), 1203-1211, 2021
62021
Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane
N Bhattarai, E Pavadai, R Pokhrel, P Baral, ML Hossen, RV Stahelin, ...
Proteins: Structure, Function, and Bioinformatics 90 (2), 340-350, 2022
52022
Evaluating protein binding interfaces with transformer networks
V Stebliankin, A Shirali, P Baral, J Shi, P Chapagain, K Mathee, ...
Nature Machine Intelligence 5 (9), 1042-1053, 2023
42023
Spike mimicry of thrombopoietin may induce thrombocytopenia in COVID-19
J Nunez-Castilla, V Stebliankin, P Baral, CA Balbin, M Sobhan, ...
BioRxiv, 2021.08. 10.455737, 2021
32021
The oncogenic circular RNA circ_63706 is a potential therapeutic target in sonic hedgehog-subtype childhood medulloblastomas
K Katsushima, R Pokhrel, I Mahmud, M Yuan, R Murad, P Baral, R Zhou, ...
Acta Neuropathologica Communications 11 (1), 38, 2023
22023
Immunoinformatic screening of Marburgvirus epitopes and computational investigations of epitope-allele complexes
P Baral, E Pavadai, Z Zhou, Y Xu, CK Tison, R Pokhrel, BS Gerstman, ...
International Immunopharmacology 111, 109109, 2022
12022
Exploring temperature-dependent conformational changes in P38 MAP kinases involved in inflammation and acute lung injury
P Baral, DJ Deredge, P Shapiro, J Hasday, AD MacKerell
Biophysical Journal 123 (3), 138a, 2024
2024
PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks
V Stebliankin, A Shirali, P Baral, P Chapagain, G Narasimhan
bioRxiv, 2023.01. 03.522623, 2023
2023
Optimization of polarizable drude nucleic acid force field using parameter reweighing via machine learning
P Baral, M Sengul, A MacKerell
ACS - Spring 2023, 2023
2023
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