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Mahdi Ghorbani
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Critical sequence hotspots for binding of novel coronavirus to angiotensin converter enzyme as evaluated by molecular simulations
M Ghorbani, BR Brooks, JB Klauda
The Journal of Physical Chemistry B 124 (45), 10034-10047, 2020
632020
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2
M Ghorbani, BR Brooks, JB Klauda
Biophysical Journal 120 (14), 2902-2913, 2021
312021
GraphVAMPNet, using graph neural networks and variational approach to Markov processes for dynamical modeling of biomolecules
M Ghorbani, S Prasad, JB Klauda, BR Brooks
The Journal of Chemical Physics 156 (18), 2022
192022
Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers
M Ghorbani, E Wang, A Krämer, JB Klauda
The Journal of Chemical Physics 153 (12), 2020
182020
Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders
M Ghorbani, S Prasad, JB Klauda, BR Brooks
The Journal of Chemical Physics 155 (19), 2021
132021
Irreversible nature of mesoscopic aggregates in lysozyme solutions
S Nikfarjam, M Ghorbani, S Adhikari, AJ Karlsson, EV Jouravleva, ...
Colloid Journal 81, 546-554, 2019
92019
Deep attention based variational autoencoder for antimicrobial peptide discovery
M Ghorbani, S Prasad, BR Brooks, JB Klauda
bioRxiv, 2022.07. 08.499340, 2022
82022
A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge
M Ghorbani, PS Hudson, MR Jones, F Aviat, R Meana-Pañeda, ...
Journal of computer-aided molecular design 35 (5), 667-677, 2021
72021
Molecular mechanism of EAG1 channel inhibition by imipramine binding to the PAS domain
ZJ Wang, M Ghorbani, X Chen, PB Tiwari, JB Klauda, TI Brelidze
Journal of Biological Chemistry 299 (12), 2023
22023
Translocation of CPP-Cargo protein fusions into Candida albicans Cells and designing for enhanced translocation with simulations
S Adhikari, M Ghorbani, K Dura, JB Klauda, AJ Karlsson
Biophysical Journal 116 (3), 513a, 2019
22019
Conformational fluctuations in β2-Microglubulin using Markov state modeling and molecular dynamics
M Ghorbani, BR Brooks, JB Klauda
The Journal of Physical Chemistry B 127 (31), 6887-6895, 2023
12023
Mechanism of EAG1 channel inhibition by imipramine binding to the PAS domain
ZJ Wang, M Ghorbani, X Chen, P Tiwari, JB Klauda, TI Brelidze
Biophysical Journal 123 (3), 252a, 2024
2024
Chlorpromazine inhibits EAG1 channels by altering the coupling between the PAS, CNBH and pore domains
M Ghorbani, ZJ Wang, X Chen, PB Tiwari, JB Klauda, TII Brelidze
bioRxiv, 2024.02. 23.581826, 2024
2024
Autoregressive fragment-based diffusion for pocket-aware ligand design
M Ghorbani, L Gendelev, P Beroza, MJ Keiser
arXiv preprint arXiv:2401.05370, 2023
2023
Unraveling the allosteric activation of GPCR using metadynamics and deep learning
M Ghorbani, S Prasad, BR Brooks, JB Klauda
Biophysical Journal 121 (3), 286a, 2022
2022
Validating Action-CSA approach for finding multiple protein folding pathways
J Min, M Ghorbani, J Lee, BR Brooks
Biophysical Journal 121 (3), 187a, 2022
2022
An Integrative MD Simulation and Network Analysis Approach to Study Glycosylation of Spike in SARS-CoV-2
M Ghorbani, BR Brooks, JB Klauda
Biophysical Journal 120 (3), 16a, 2021
2021
Mechanism of Degradation of Histatin 5 Peptide by Secreted Aspartic Proteases (SAPS) of C. Albicans
M Ghorbani, JB Klauda, BR Brooks
Biophysical Journal 118 (3), 534a-535a, 2020
2020
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2 (preprint)
M Ghorbani, BR Brooks, JB Klauda
2020
Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations (preprint)
M Ghorbani, BR Brooks, JB Klauda
2020
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Articles 1–20