About
With a Ph.D. in Chemistry and extensive experience spanning over eight years in computational chemistry, I specialize in driving computer aided drug discovery through the integration of quantum mechanics, molecular dynamics (MD), and AI-based methodologies. My career is marked by a proven track record in applying GPU-accelerated MD simulations, free energy perturbation methods, and developing computational models to address critical challenges in drug discovery.
At the core of my expertise is a deep proficiency in quantum chemistry and molecular dynamics simulations, where my contributions have significantly advanced molecular modeling hypotheses and drug discovery endeavors. My collaborative spirit shines in multidisciplinary projects, working seamlessly with ML experts, software engineers, and a broad spectrum of scientists to pioneer groundbreaking solutions.
My technical skills include the following:
Quantum Chemistry codes: Gaussian, Orca, Gamess-US
Molecular Dynamics: Amber, Gromacs
Monte Carlo: ROSETTA
Machine learning software: Alphafold, ESMfold, Omegafold, Alphamissense, Equibind
Visualization software: Pymol, MOE, VMD, Chimera, Gaussview, Chemcraft, Avagadro,
Plotting software and data analysis: Origin, Gnuplot, Matlab
Programming languages: C++, Python, and BASH scripting
Operating systems: Linux, Windows and Mac
Deep learning: Alphafold, Alphamissense, Diffdock, Equibind, RF-diffusion, Protein MPNN
At the core of my expertise is a deep proficiency in quantum chemistry and molecular dynamics simulations, where my contributions have significantly advanced molecular modeling hypotheses and drug discovery endeavors. My collaborative spirit shines in multidisciplinary projects, working seamlessly with ML experts, software engineers, and a broad spectrum of scientists to pioneer groundbreaking solutions.
My technical skills include the following:
Quantum Chemistry codes: Gaussian, Orca, Gamess-US
Molecular Dynamics: Amber, Gromacs
Monte Carlo: ROSETTA
Machine learning software: Alphafold, ESMfold, Omegafold, Alphamissense, Equibind
Visualization software: Pymol, MOE, VMD, Chimera, Gaussview, Chemcraft, Avagadro,
Plotting software and data analysis: Origin, Gnuplot, Matlab
Programming languages: C++, Python, and BASH scripting
Operating systems: Linux, Windows and Mac
Deep learning: Alphafold, Alphamissense, Diffdock, Equibind, RF-diffusion, Protein MPNN
Publications
Powered by Google Scholar| TITLE | CITED BY | YEAR |
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Ligand-assisted metal-centered electrocatalytic hydrogen evolution upon reduction of a bis (thiosemicarbazonato) Ni (II) complex
R Jain, AA Mamun, RM Buchanan, PM Kozlowski, CA Grapperhaus
Inorganic chemistry 57 (21), 13486-13493
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79 | 2018 |
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Trace metals concentrations at the atmosphere particulate matters in the Southeast Asian Mega City (Dhaka, Bangladesh)
MD Islam, SS Majumder, AA Mamun, MD Khan, MA Rahman, A Salam
Open Journal of Air Pollution 4 (02), 86-98
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51 | 2015 |
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Photolytic properties of the biologically active forms of vitamin B12
MJ Toda, P Lodowski, AA Mamun, M Jaworska, PM Kozlowski
Coordination Chemistry Reviews 385, 20-43
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42 | 2019 |
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Mechanism of the photo-induced activation of Co-C bond in methylcobalamin-dependent methionine synthase-
AP Ghosh, AA Mamun, P Lodowski, M Jaworska, PM Kozlowski
Journal of Photochemistry and Photobiology B: Biology 189, 306-317
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29 | 2018 |
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Utilizing charge effects and minimizing intramolecular proton rearrangement to improve the overpotential of a thiosemicarbazonato zinc HER catalyst
SP Cronin, AA Mamun, MJ Toda, MS Mashuta, Y Losovyj, PM Kozlowski, ...
Inorganic Chemistry 58 (19), 12986-12997
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25 | 2019 |
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Mechanism of Light Induced Radical Pair Formation in Coenzyme B<sub>12</sub>-Dependent Ethanolamine Ammonia-Lyase
AA Mamun, MJ Toda, P Lodowski, M Jaworska, PM Kozlowski
ACS Catalysis 8 (8), 7164-7178
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24 | 2018 |
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Photolytic Cleavage of Co–C Bond in Coenzyme B<sub>12</sub>-Dependent Glutamate Mutase
AA Mamun, MJ Toda, P Lodowski, PM Kozlowski
The Journal of Physical Chemistry B 123 (12), 2585-2598
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23 | 2019 |
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Why is CarH photolytically active in comparison to other B12-dependent enzymes?
MJ Toda, A Al Mamun, P Lodowski, PM Kozlowski
Journal of Photochemistry and Photobiology B: Biology 209, 111919
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21 | 2020 |
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Can photolysis of the Co-C bond in coenzyme B12-dependent enzymes be used to mimic the native reaction?
AA Mamun, MJ Toda, PM Kozlowski
Journal of Photochemistry and Photobiology B: Biology
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16 | 2018 |
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Acquired Secondary <i>HER2</i> Mutations Enhance HER2/MAPK Signaling and Promote Resistance to HER2 Kinase Inhibition in Breast Cancer
A Marín, AA Mamun, H Patel, H Akamatsu, D Ye, DR Sudhan, L Eli, ...
Cancer research 83 (18), 3145-3158
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11 | 2023 |
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How does the mutation in the cap domain of methylcobalamin-dependent methionine synthase influence the photoactivation of the Co–C bond?
AP Ghosh, A Al Mamun, PM Kozlowski
Physical Chemistry Chemical Physics 21 (37), 20628-20640
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9 | 2019 |
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Resonance Raman investigation of dithionite‐reduced cobalamin
K Mieda‐Higa, AA Mamun, T Ogura, T Kitagawa, PM Kozlowski
Journal of Raman Spectroscopy
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7 | 2020 |
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Personalized query expansion for web search using social keywords
SM Sarwar, MA Abedin, AHMS Ullah, A Al Mamun
Proceedings of International Conference on Information Integration and Web …
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6 | 2013 |
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Electronic and photolytic properties of hydridocobalamin
MJ Toda, P Lodowski, A Al Mamun, PM Kozlowski
Journal of Photochemistry and Photobiology B: Biology 224, 112295
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5 | 2021 |
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Photoproduct formation in coenzyme B12-dependent CarH via a singlet pathway
MJ Toda, P Lodowski, A Al Mamun, PM Kozlowski
Journal of Photochemistry and Photobiology B: Biology 232, 112471
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4 | 2022 |
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Light-induced activation of organo-metallic Co-C bond in MeCbl-dependent methionine synthase-QM/MM study
AP Ghosh, A Al Mamun, PM Kozlowski
Biophysical Journal 116 (3), 67a-68a
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3 | 2019 |
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Computational modeling of photolysis and catalysis reactions in vitamin b12-dependent enzymes.
AA Mamun
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2 | 2020 |
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Acquired secondary HER2 mutations enhance HER2/MAPK signaling and promote resistance to HER2 kinase inhibition in HER2-mutant breast cancer
A Marin, AA Mamun, H Akamatsu, D Ye, DR Sudhan, BP Brown, L Eli, ...
bioRxiv, 2022.09. 23.509246
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1 | 2022 |
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VUStruct: a compute pipeline for high throughput and personalized structural biology
CW Moth, JH Sheehan, A Al Mamun, RM Sivley, A Gulsevin, D Rinker, ...
bioRxiv
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2024 | |
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Integrative structural models of oncogenic mutants within the trans-and juxta-membrane region of human epidermal growth factor receptors (HERs)
C Mercado, AA Mamun, Y Park, CM Lovly, J Meiler, K Ledwitch
Cancer Research 83 (7_Supplement), 3173-3173
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2023 | |
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