Publications
Selected Key Publications
Dominguez-Medina, S.; Fostner, S.; Defoort, M.; Sansa, M.; Stark, A. K.; Halim, M. A.; Vernhes, E.; Gely, M.; Jourdan, G.; Alava, T.; Boulanger, P., Masselon, C.; Hentz, S. ‘Neutral Mass Spectrometry of Virus Capsid above 100 MDa with Nanomechnical Resonators’. Science, 2018, 362, 918-922. Publisher: American Association for the Advancement of Science, USA.
Featured in Chemistry World: Mass spec goes massive weighing huge virus particles https://bit.ly/2PacJ0G
*Pansieri, J.; *Halim, M. A.; Vendrely, C.; Dumoulin, M.; Moulin, M.; Chierici, S.; Denti, S.; Dagany, X.; Dugourd, P. ; Marquette, C.; Antoine, R.; Forge, V. “Mass and charge distributions of entire amyloid fibers involved in neurodegenerative diseases : Mapping polymorphism effects and population heterogeneity.” Chemical Science. 2018, 9, 2791-2796. DOI:10.1039/C7SC04542E, Publisher: Royal Society of Chemistry, UK. *Co-first author.
Featured in Chemical & Engineering News (C&CN): Charge detection mass spectrometry measures molecular structures too big for regular mass spec, https://bit.ly/2QAtYwo
Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization.” Journal of American Society for Mass Spectrometry 2016, 27, 1435-1442. doi:10.1007/s13361-016-1419-8 (Cover Article) Publisher: American Society for Mass Spectrometry, USA
Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “Ultraviolet, Infrared and High-Low Energy Photodissociation of Post-Translationally Modified Peptides.” Journal of American Society for Mass Spectrometry, 2018, 29, 270–283. DOI: 10.1007/s13361-017-1794-9. Publisher: American Society for Mass Spectrometry, USA
Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “213 nm Ultraviolet Photodissociation on Peptide Anions: Radical-Directed Fragmentation Patterns.” Journal of American Society for Mass Spectrometry 2016, 27, 474-486. DOI: 10.1007/s13361-015-1297-5. Publisher: American Society for Mass Spectrometry, USA
Halim, M. A.; Clavier, F.; Dagany, X.; Kerleroux, M.; Dugourd, P.; Dunbar, R.; Antoine, R. “Fragmentation of Single Megadalton Polymer Ions in a Gated Electrostatic Ion Trap. The Added Value of Statistical Analysis of Individual Events.” Physical Chemistry Chemical Physics. 2018, 20, 11959-11966 DOI:10.1039/C8CP00404H, Publisher: Royal Society of Chemistry, UK
Halim, M. A.; Bertorelle, F.; Doussineau, T.; and Antoine, R. ‘Direct Molecular Weight Distribution of Calf-Thymus DNAs and Fragmentation under Ultrasonic and Low-Energy IR Irradiations. A Charge Detection Mass Spectrometry Investigation.’ Rapid Communication in Mass Spectrometry, 2019, 33 (S1), 35-39. https://doi.org/10.1002/rcm.8204. Publisher: John Wiley & Sons, USA
2023
(95) Stewart, J.; Shawon, J.; Ali, M. A.; Shahinuzzaman, A.; Rupa, S.; Williams, B.; Al-Adhami, T.; Jia, Bourque, C.; R.; Faddis, R.; Stone, K.; Sufian, M. A.; Islam, R.; McShan, A. C.; Rahman, K. M.; Halim, M. A. Antiviral Peptides Inhibiting the Main Protease of SARS-CoV-2 Investigated by Computational Screening and In-Vitro Protease Assay. Journal of Peptide Science 2023. Accepted.
(94) Faddis, R.; Du, S.; Stewart, J.; Hasan, M. M.; Lewit. N. Ali, M. A.; White, C. B.; Okoto, P.; Thallapuranam, S.; Halim, M. A. 'Molecular Modelling, Synthesis, and In-Vitro Assay to Identify Potential Antiviral Peptides targeting the 3-Chymotrypsin-like Protease of SARS-CoV-2' International Journal of Peptide Research and Therapeutics, 2023, 29, 89 https://doi.org/10.1007/s10989-023-10563-w
(93) Rub, M. A.; Azum, N.; Alfaifi, S. Y. M.; Sakib, M. M. H., Ali, M. A.; Mahbub, S.; Haim, M. A.; Hoque, M. A.; Asiri, A. M.
'Assessment of mixed micellization behavior of amitriptyline hydrochloride and TX-165 surfactant mixture in various media (aqueous/NaCl/urea)', Journal of Molecular Liquids, 2023, In press. https://doi.org/10.1016/j.molliq.2023.122073 Publisher: Elsevier, Netherlands.
(92) Ali, M. A.; Kaium, M. A.; Uddin, S. N.; Uddin, M. J.; Olawuyi, O.; Campbell, A. D. Jr.; Saint-Louis, C. J.; Halim, M. A. Elucidating the Structure, Dynamics, and Interaction of a Choline Chloride and Citric Acid Based Eutectic System by Spectroscopic and Molecular Modeling Investigations. ACS Omega 2023. https://doi.org/10.1021/acsomega.3c04570
(91) Akter, S.; Islam, M. J.; Ali, M. A.; Tashrif, M. Z.; Uddin, M. J.; Ullah, M. O.; Halim, M. A. 'Structure and dynamics of whole-sequence homology model of ORF3a protein of SARS-CoV-2: An insight from microsecond molecular dynamics simulations', Journal of Biomolecular Structure and Dynamics, 2023, DOI: 10.1080/07391102.2023.2236715, Publisher: Taylor and Francis, UK
(90) Uddin, M. J.; Akhter, H.; Chowdhury, U.; Mawah, J.; Karim, S. T.; Jomel, M.; Islam, M. S.; Islam, M. R.; Onin, L. A. B.; Ali, Halim, M. A. Large Scale Peptide Screening against Main Protease of SARS CoV‐2. Journal of Computational Chemistry 2023, 44(8), 869-947. https://doi.org/10.1002/jcc.27050. Publisher: John Wiley & Sons, USA
(89) Hossain, Md. S.; Shovon, Md. T. I.; Hasan, Md. R.; Hakim, F. T.; Hasan, M. M.; Esha, S. A.; Tasnim, S.; Nazir, Md. S.; Akhter, F.; Ali, M. A.; Halim, M. A. Therapeutic Potential of Antiviral Peptides against the NS2B/NS3 Protease of Zika Virus. ACS Omega 2023, 8 (38), 35207–35218. https://doi.org/10.1021/acsomega.3c04903.
(88) Islam, S.; Parves, M. R.; Islam, M. J.; Ali, M. A.; Efaz, F. M.; Hossain, M. S.; Ullah, M. O.; Halim, M. A. 'Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study' Journal of Biomolecular Structure and Dynamics 2023. https://doi.org/10.1080/07391102.2023.2228919 Publisher: Taylor and Francis, UK
(87) Islam, M. J.; Islam, N. N.; Alom, M. S.; Kabir, M.; Halim, M. A. 'A Review on Structural, Non-Structural, and Accessory Proteins of SARS-CoV-2: Highlighting Drug Target Sites'. Immunobiology 2023, 152302. Publisher: Elsevier, Netherlands.
(86) Hossen, M. R.; Biswas, S.; Ali, M. A.; Halim, M. A.; Ullah, M. O. 'In silico peptide-based therapeutics against human colorectal cancer by the activation of TLR5 signaling pathways', Journal of Molecular Modelling, 2023, 29, 35. Publisher: Springer
(85) Biswas, B.; Hossen, M. R.; Akter, S.; Ali, M. A., Halim, M. A.; Ullah, M. O. ‘Structural dynamics and functional analysis of Saprolegnia parasitica chitin synthases 5 in a phospholipid bilayer’, Journal of Biomolecular Structure and Dynamics 2023. DOI: 10.1080/07391102.2023.2193993 Publisher: Taylor and Francis, UK
2022
(84) Jiang, L. X.; Plath, L. D.; Halim, M. A.; Friedrich, S.; Bier, M. E. 'Anatomy of Protein Electrospray Ionization Mass Spectra by Superconducting Tunnel Junction Mass and Energy Spectrometry' Analytical Chemistry 2022, 94 (13), 5284-5292 DOI: 10.1021/acs.analchem.1c05074 Publisher: American Chemical Society, USA.
(83) Rahman, M. S.; Roy, R.; Montoya, C.; Halim, M. A.; Raynie, D. E. Acidic and Basic Amino Acid-Based Novel Deep Eutectic Solvents and Their Role in Depolymerization of Lignin. Journal of Molecular Liquids 2022, 362, 119751. https://doi.org/https://doi.org/10.1016/j.molliq.2022.119751. Publisher: Elsevier, Netherlands.
(82) Raha, F. K.; Hasan, J.; Ali, M. A.; Fakayode, S. O.; Halim, M. A. Exploring the molecular level interaction of Xenoestrogen phthalate plasticisers with oestrogen receptor alpha (ERα) Y537S mutant, Molecular Simulation, 2022, DOI: 10.1080/08927022.2022.2101675 Publisher: Taylor & Francis, UK
(81) Mahdi, I.; Yeasmin, H.; Hossain, I.; Badhan, R. M.; Ali, M. A.; Kaium, M.; Islam, R.; Sufian, M.; Halim, M. A., Potential antiviral peptides against the nucleoprotein of SARS-CoV-2, Chemical Paper, 2022, In press, https://link.springer.com/article/10.1007/s11696-022-02514-4 Publisher: Springer
(80) Hasan, M. M.; Shahriar, I.; Ali, M. A.; Halim, M. A.; Ehsan, Q. M. Experimental and computational studies on transition metals interaction with Leucine and Isoleucine, Journal of Molecular Structure, 2022, 1270, 133862. https://doi.org/10.1016/j.molstruc.2022.133862 Publisher: Elsevier, Netherlands.
(79) Zohora, F. T.; Azam, A. T. M.; Ahmed, S.; Rahman, K. M.; Halim, M. A.; Anwar, M.; Sohrab, M.; Tabassum, F.; Hasan, C. M.; Ahsan, M. Isolation and In Silico Prediction of Potential Drug-like Compounds with a New Dimeric Prenylated Quinolone Alkaloid from Zanthoxylum Rhetsa (Roxb.) Root Extracts Targeted against SARS-CoV-2 (Mpro). Molecules 2022, 27 (23), 8191
(78) Uddin, M. J.; Faraone, I.; Haque, M. A.; Rahman, M. M.; Halim, M. A.; Sönnichsen, F. D.; Çiçek, S. S.; Milella, L.; Zidorn, C. Insights into the leaves of Ceriscoides campanulata: Natural proanthocyanidins alleviate diabetes, inflammation, and esophageal squamous cell cancer via in vitro and in silico models, Fitoterapia, 2022, 158, 105164, https://doi.org/10.1016/j.fitote.2022.105164. Publisher: Elsevier, Netherlands.
(77) Rahman, M. S.; Kyeremateng, J.; Saha, M.; Asare, S.; Uddin, N.; Halim, M. A.; Raynie, D. E. Evaluation of the experimental and computed properties of choline chloride-water formulated deep eutectic solvents, Journal of Molecular Liquids 2022, 350, 118520. https://doi.org/10.1016/j.molliq.2022.118520. Publisher: Elsevier, Netherlands.
(76) Haque, M. A; Islam, K. B.; Mahbub, S.; Masood Khan, J.; Hossian, J.; Anamul Hoque, M.; Halim, M. A.; Majibur Rahman, M.; Ahmad, A.; Ahmed, M. Z. Impact of Ethanol and NaCl on the Acid Yellow Dye Mediated Self-Aggregation of Sodium Dodecyl Sulfate: A Combined Investigation by Conductivity and Molecular Dynamics Simulation. Journal of Molecular Liquids 2022, 345, 117819. https://doi.org/https://doi.org/10.1016/j.molliq.2021.117819 Publisher: Elsevier, Netherlands.
(75) Omor Faruk Patwary, M.; Mahbubur Rahman, M.; Khalid Bin Islam, M.; Ackas Ali, M.; Halim, M. A.; Ahmed, F. 'Probing the Non-Bonding Interaction of Small Molecules with Graphene Oxide Using DFT Based Vibrational Circular Dichroism.' Computational and Theoretical Chemistry 2022, 1207, 113503. 8 https://doi.org/https://doi.org/10.1016/j.comptc.2021.113503. Publisher: Elsevier, Netherlands.
(74) Khan, A. T.; Chowdhury, G. M.; Hafsah, J.; Maruf, M.; Raihan, M. R. H.; Chowdhury, M. T.; Nawal, N.; Tasnim, N.; Saha, P.; Roy, P.; Tabassum, R.; Rodrigues, S. P.; Hasan, W.; Samanta, Z. T.; Kamal, S.; Nazir, M. S.; Ali, M. A.; Halim, M. A.* A Student Led Computational Screening of Peptide Inhibitors against Main Protease of SARS-CoV-2. Biochemistry and Molecular Biology Education 2022, 50, 7-20. https://doi.org/https://doi.org/10.1002/bmb.21580. Publisher: John Wiley & Sons, USA
(73) Sultana, M. U. C.; Uddin, M. G.; Hossain, M. B.; Ali, M. A.; Sonia, Z. F.; Kamal, S.; Halim, M. A.* Molecular Dynamics Investigation of Ivermectin Bound to Importin Alpha/Beta Heterodimer. Molecular Simulation 2022, 48, 314-321. https://doi.org/10.1080/08927022.2021.2015066. Publisher: Taylor & Francis, UK
2021
(72) Efaz, F. Md.; Islam, S.; Talukder, S. A.; Akter, S.; Tashrif, Md. Z.; Ali, Md. A.; Sufian, Md. A.; Parves, Md. R.; Islam, Md. J.; Halim, M. A.* Repurposing Fusion Inhibitor Peptide against SARS-CoV-2. Journal of Computational Chemistry 2021, 42, 2283-2293. https://doi.org/https://doi.org/10.1002/jcc.26758. Publisher: John Wiley & Sons, USA
(71) Rain, M. I.; Iqbal, H.; Saha, M.; Ali, M. A.; Chohan, H. K.; Rahman, M. S.; Halim, M. A. A Comprehensive Computational and Principal Component Analysis on Various Choline Chloride-Based Deep Eutectic Solvents to Reveal Their Structural and Spectroscopic Properties. Journal of Chemical Physics 2021, 155 (4), 44308. https://doi.org/10.1063/5.0052569. Publisher: American Institute of Physics (AIP), USA.
(70) Hossain Sakib, M. M.; Nishat, A. A.; Islam, M. T.; Raihan Uddin, M. A.; Iqbal, M. S.; Bin Hossen, F. F.; Ahmed, M. I.; Bashir, M. S.; Hossain, T.; Tohura, U. S.; Saif, S. I.; Jui, N. R.; Alam, M.; Islam, M. A.; Hasan, M. M.; Sufian, M. A.; Ali, M. A.; Islam, R.; Hossain, M. A.; Halim, M. A. Computational Screening of 645 Antiviral Peptides Against the Receptor-Binding Domain of the Spike Protein in SARS-CoV-2. Computers in Biology and Medicine 2021, 136, 104759. https://doi.org/10.1016/j.compbiomed.2021.104759. Publisher: Elsevier, Netherlands
(69) Ali, M. A.; Rahman, M. S.; Roy, R.; Gambill, P.; Raynie, D. E.; Halim, M. A. Structure Elucidation of Menthol-Based Deep Eutectic Solvent Using Experimental and Computational Techniques. Journal of Physical Chemistry A 2021, 125 (12), 2402–2412. https://doi.org/10.1021/acs.jpca.0c10735. Publisher: American Chemical Society, USA.
(68) Khan, A. T.; Chowdhury, G. M.; Hafsah, J.; Maruf, M.; Raihan, M. R. H.; Chowdhury, M. T.; Nawal, N.; Tasnim, N.; Saha, P.; Roy, P.; Tabassum, R.; Rodrigues, S. P.; Hasan, W.; Samanta, Z. T.; Kamal, S.; Nazir, M. S.; Ali, M. A.; Halim, M. A. A Student Led Computational Screening of Peptide Inhibitors against Main Protease of SARS-CoV-2. Biochemistry and Molecular Biology Education 2021, n/a (n/a). https://doi.org/https://doi.org/10.1002/bmb.21580.
(67) Uddin, M. J.; Russo, D.; Rahman, M. M.; Uddin, S. B.; Halim, M. A.; Zidorn, C.; Milella, L.Anticholinesterase Activity of Eight Medicinal Plant Species: In Vitro and In Silico Studies in the Search for Therapeutic Agents against Alzheimer’s Disease. Evidence-Based Complement. Altern. Med. 2021, 2021, 9995614. https://doi.org/10.1155/2021/9995614. Publisher: Hindawi, Egypt.
(66) Khan, M. T.; Islam, M. J.; Parihar, A.; Islam, R.; Jerin, T. J.; Dhote, R.; Ali, M. A.; Laura, F. K.; Halim, M. A. Immunoinformatics and Molecular Modeling Approach to Design Universal Multi-Epitope Vaccine for SARS-CoV-2. Informatics Med. Unlocked 2021, 100578. https://doi.org/https://doi.org/10.1016/j.imu.2021.100578. Publisher: Elsevier, Netherlands
(65) Mamun, A. al; Akter, F.; Khan, M.; Ahmed, S. S.; Uddin, Md. G.; Tasfia, N. T.; Efaz, F. Md.; Ali, M. A.; Sultana, M. U. C.; Halim, M. A. Identification of Potent Inhibitors against Transmembrane Serine Protease 2 for Developing Therapeutics against SARS-CoV-2. Journal of Biomolecular Structure and Dynamics 2021, 1–13. https://doi.org/10.1080/07391102.2021.1980109. Publisher: Taylor and Francis, UK
(64) Rahman, M. S.; Roy, R.; Jadhav, B.; Hossain, M. N.; Halim, M. A.; Raynie, D. E. Formulation, Structure, and Applications of Therapeutic and Amino Acid-Based Deep Eutectic Solvents: An Overview. Journal of Molecular Liquids 2021, 321,114745. https://doi.org/https://doi.org/10.1016/j.molliq.2020.114745. Publisher: Elsevier, Netherlands
(63) Rahman, M. M.; Biswas, S.; Islam, K. J.; Paul, A. S.; Mahato, S. K.; Ali, M. A.; Halim, M. A. Antiviral Phytochemicals as Potent Inhibitors against NS3 Protease of Dengue Virus. Computers in Biology and Medicine 2021, 134, 104492. https://doi.org/https://doi.org/10.1016/j.compbiomed.2021.104492. Publisher: Elsevier, Netherlands
(62) Mahmud, S.; Islam, M. J.; Parves, M. R.; Khan, M. A.; Tabussum, L.; Ahmed, S.; Ali, M. A.; Fakayode, S. O.; Halim, M. A. Designing Potent Inhibitors against the Multidrug Resistance P-Glycoprotein. Journal of Biomolecular Structure & Dynamics, 2021. In press, https://doi.org/10.1080/07391102.2021.1930159.Publisher: Taylor and Francis, UK
(61) Rahim, M. A.; Mahbub, S.; Ahsan, S. M. A.; Manawwer, A.; Saha, M.; Shahriar, I.; Rana, S.; Halim, M. A.; Hoque, M. A.; Kumar, D.; Khan, J. M.; ‘Conductivity, cloud point and molecular dynamics investigations of the interaction of surfactants with ciprofloxacin hydrochloride drug: Effect of electrolytes’ Journal of Molecular Liquids, 2021, 322, 114683. https://doi.org/10.1016/j.molliq.2020.114683 Publisher: Elsevier, Netherlands
(60) Shawon, J.; Khan, A. M.; Shahriar, I.; Halim, M. A. Improving the Binding Affinity and Interaction of 5-Pentyl-2-Phenoxyphenol against Mycobacterium Enoyl ACP Reductase by Computational Approach. Informatics Med. Unlocked 2021, 23, 100528. https://doi.org/10.1016/j.imu.2021.100528. Publisher: Elsevier, Netherlands
(59) Islam, R.; Parves, R.; Paul, A. S.; Uddin, N.; Rahman, M. S.; Mamun, A. Al; Hossain, M. N.; Ali, M. A.; Halim, M. A. ‘A Molecular Modeling Approach to Identify Effective Antiviral Phytochemicals against the Main Protease of SARS-CoV-2.’ Journal of Biomolecular Structure & Dynamics 2021, 39 (9), 3213-3224. https://doi.org/10.1080/07391102.2020.1761883. Publisher: Taylor and Francis, UK
(58) Zahan, R.; Ahmed, S.; Sharmin, T.; Halim, M. A.; Rahi, M. S.; Sheikh, M. C.; Miyatake, R.; Zangrando, E.; Naz, T.; Islam, M. A.-A.-A.-A.; Reza, M. A. Synthesis of Bis[Benzyl-N′-Hydrazinecarbodithioato-Κ2 N′,S]Nickel(II) Complex as a Novel Lead Molecule for Cancer Treatment. Appl. Organomet. Chem. 2021, 35(1), e6036. https://doi.org/10.1002/aoc.6036. Publisher: John Wiley & Sons, USA
2020
(57) Chowdhury, S. M.; Talukder, S. A.; Khan, A. M.; Afrin, N.; Ali, M. A.; Islam, R.; Parves, R.; Mamun, A. A.; Sufian, M. A.; Hossain, M. N.; Hossain, M. A.; Halim, M. A. ‘Antiviral Peptides as Promising Therapeutics against SARS-CoV-2’ Journal of Physical Chemistry B, 2020, 124, 9785-9792. https://doi.org/10.1021/acs.jpcb.0c05621 Publisher: American Chemical Society, USA.
(56) Saha, M.; Rahman, M. S; Hossain, M. N.; Raynie, D. E.; Halim, M. A.; ‘Molecular and Spectroscopic Insights of a Choline Chloride Based Therapeutic Deep Eutectic Solvent’ 2020, 124, 4690–4699. The Journal of Physical Chemistry A, DOI: 10.1021/acs.jpca.0c00851 Publisher: American Chemical Society, USA
(55) Paul, A. S.; Islam, R.; Parves, R.; Mamun, A. Al; Shahriar, I.; Hossain, M. I.; Hossain, M. N.; Ali, M. A.; Halim, M. A. ‘Cysteine focused covalent inhibitors against the main protease of SARS-CoV-2.’ Journal of Biomolecular Structure & Dynamics 2020, 1-20. In press, DOI: 10.1080/07391102.2020.1831610 Publisher: Taylor and Francis, UK
(54) Almatarneh, M.H.; Alnajajrah, A.; Altarawneh, M.; Zhao, Y.; Halim, M. A. Computational mechanistic study of the unimolecular dissociation of ethyl hydroperoxide and its bimolecular reactions with atmospheric species. Scientific Report 2020, 10, 15025. https://doi.org/10.1038/s41598-020-71881-3 Publisher: Nature Publishing Group, UK.
(53) Mahtarin, R.; Islam, S.; Islam, M. J.; Ullah, M. U.; Ali, M. A.; Halim, M. A. Structure and dynamics of membrane protein in SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 2020, 1-14, In press DOI: 10.1080/07391102.2020.1861983 Publisher: Taylor and Francis, UK
(52) Ahmed, S.; Mahtarin, R.; Ahmed, S. S.; Akter, S.; Islam, M. S.; Mamun, A. Al; Islam, R.; Hossain, M. N.; Ali, M. A.; Sultana, M. U. C.; Halim, M. A. Investigating the Binding Affinity, Interaction, and Structure-Activity-Relationship of 76 Prescription Antiviral Drugs Targeting RdRp and Mpro of SARS-CoV-2. Journal of Biomolecular Structure & Dynamics 2020, 1–16. https://doi.org/10.1080/07391102.2020.1796804 Publisher: Taylor and Francis, UK
(51) Rahman, M. M.; Saha, T.; Islam, K. J.; Suman, R. H.; Biswas, S.; Rahat, E. U.; Hossen, M. R.; Islam, R.; Hossain, M. N.; Mamun, A. Al; Ackas, M.; Halim, M. A. Virtual Screening, Molecular Dynamics and Structure--Activity Relationship Studies to Identify Potent Approved Drugs for Covid-19 Treatment. Journal of Biomolecular Structure & Dynamics. 2020, 1–11. https://doi.org/10.1080/07391102.2020.1794974 Publisher: Taylor and Francis, UK
(50) Ahmed, S.; Islam, N.; Shahinozzaman, M.; Fakayode, S. O.; Afrin, N.; Halim, M. A. ‘Virtual Screening, Molecular Dynamics, Density Functional Theory and Quantitative Structure Activity Relationship Studies to Design Peroxisome Proliferator-Activated Receptor-γ Agonists as Anti-Diabetic Drugs’ Journal of Biomolecular Structure & Dynamics 2020, 1–15. https://doi.org/10.1080/07391102.2020.1714482. Publisher: Taylor and Francis, UK
(49) Amin, M. R.; Alissa, S. A.; Saha, M.; Hossian, J.; Shahriar, I.; Halim, M. A.; Hoque, M. A.; Alothman, Z. A.; Wabaidur, S. M.; Kabir, S. E. ‘Investigation of the Impacts of Temperature and Electrolyte on the Interaction of Cationic Surfactant with Promethazine Hydrochloride: Combined Conductivity and Molecular Dynamics Studies.’ Journal of Molecular Liquids 2020, 113246. https://doi.org/10.1016/j.molliq.2020.113246. Publisher: Elsevier, Netherlands
(48) Aktar, S.; Saha, M.; Mahbub, S.; Halim, M. A.; Rub, M. A.; Hoque, M. A.; Islam, D. M. S.; Kumar, D.; Alghamdi, Y. G.; Asiri, A. M. ‘Influence of Polyethylene Glycol on the Aggregation/Clouding Phenomena of Cationic and Non-Ionic Surfactants in Attendance of Electrolytes (NaCl & Na2SO4): An Experimental and Theoretical Analysis.’ Journal of Molecular Liquids 2020, 306, 112880. https://doi.org/https://doi.org/10.1016/j.molliq.2020.112880. Publisher: Elsevier, Netherlands
(47) Nasreen, W.; Sarker, S.; Sufian, M. A.; Opo, F. A. D. M.; Shahriar, M.; Akhter, R.; Halim, M. A. ‘A Possible Alternative Therapy for Type 2 Diabetes Using Myristica Fragrans Houtt in Combination with Glimepiride: In Vivo Evaluation and in Silico Support.’ Zeitschrift für Naturforsch. C 2020, 75 (3–4), 103–112. https://doi.org/https://doi.org/10.1515/znc-2019-0134. Publisher: DE GRUYTER GmBH, Germany.
(46) Shahinozzaman, M.; Ishii, T.; Ahmed, S.; Halim, M. A.; Tawata, S. ‘A Computational Approach to Explore and Identify Potential Herbal Inhibitors for the P21-Activated Kinase 1 (PAK1).’ Journal of Biomolecular Structure & Dynamics 2020, 38 (12), 3514-3526. https://doi.org/10.1080/07391102.2019.1659855. Publisher: Taylor and Francis, UK
(45) Uddin, N.; Ahmed, S.; khan, M. A. K.; Hoque, M. M.; Halim, M. A. ‘Halogenated Derivatives of Methotrexate as Human Dihydrofolate Reductase Inhibitor in Cancer Chemotherapy’ the Journal of Biomolecular Structure & Dynamics, 2020. 38 (3), 901-917. https://doi.org/10.1080/07391102.2019.1591302 Publisher: Taylor and Francis, UK
2019
(44) Halim, M. A.; Bertorelle, F.; Doussineau, T.; and Antoine, R. ‘Direct Molecular Weight Distribution of Calf-Thymus DNAs and Fragmentation under Ultrasonic and Low-Energy IR Irradiations. A Charge Detection Mass Spectrometry Investigation.’ Rapid Communication in Mass Spectrometry, 2019, 33 (S1), 35-39. https://doi.org/10.1002/rcm.8204. Publisher: John Wiley & Sons, USA
(43) Islam, J.; Khan, A. M.; Parves, R. Halim, M. A. "Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking and Molecular Dynamics Simulation" Scientific Report, 2019, 9, 16426. DOI: 10.1038/s41598-019-52308-0. Publisher: Nature Publishing Group, UK.
(42) Junaid, M.; Alam, M. J.; Hossain, M, K.; Ullah, M. O.; Halim, M. A. ‘Metal Based Donepezil Analogues Designed to Inhibit Human Acetylcholinesterase for Alzheimer's disease.’ PLOS ONE, 2019, 14(2): e0211935 https://doi.org/10.1371/journal.pone.0211935 Publisher: Public Library of Science, California, USA.
(41) Ahmed, F.; Molla, M. R.; Shahriar, I.; Saha, M.; Rahman, M. S.; Hoque, M. A.; Halim, M. A.; Rub, M. A.; Asiri A. M.; ‘Aggregation Behavior of Cetyldimethylethylammonium Bromide under the Influence of Bovine Serum Albumin in Aqueous/ Electrolyte Solutions at Various Temperatures and Compositions: Conductivity and Molecular Dynamics Study’, RSC Advances, 2019, 9, 6556-6567. DOI: 10.1039/C9RA00070D. Publisher: Royal Society of Chemistry, UK.
(40) Shahriar, I.; Iqfath, M.; Islam, K. B.; Rahman, A.; Halim, M. A.* “Solvent Effect on Vibrational Circular Dichroism of Chiral Amino Acids” Theoretical Chemistry Accounts, 2019, 138, 32. https://doi.org/10.1007/s00214-019-2419-0 Publisher: Springer, Germany
(39) Mahbub, S.; Shahriar, I.; Saha, M.; Molla, M. R.; Halim, M. A.; Hoque, M. A.; Rub, M. A.; ‘Conductometric and Molecular Dynamics studies of the Aggregation behavior of sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB) in aqueous and electrolytes solution’ Journal of Molecular Liquids, 2019, 283, 263-275. https://doi.org/10.1016/j.molliq.2019.03.045 Publisher: Elsevier, Netherlands
(38) Begum, N.; Islam, M. T.; Hossain, S. R.; Bhuyan, G. S.; Halim, M. A.; Shahriar, I.; Sarker, S. K.; Rahat, A.; Haque, S.; Konika, T. K; Qadri, S. K.; Islam, M. S.; Sultana, R.; Begum, S.; Sultana, S.; Saha, N.; Hasan, M.; Hasanat, M. A.; Banu, H.; Shekhar, H. U.; Chowdhury, E. K.; Sajib, A. A.; Islam, A.; Qadri, S. S.; Qadri, F.; Akhteruzzaman, S.; Mannoor, K. “Mutation spectrum in TPO gene of Bangladeshi patients with thyroid dyshormonogenesis and analysis of the effects of different mutations on the structural features and functions of TPO protein through in silico approach” BioMed Research International, 2019, Article ID 9218903, 1-18. https://doi.org/10.1155/2019/9218903. Publisher: Hindawi, Egypt.
(37) Tania, M.; Shawon, J.; Saif, K.; Rudolf Kiefer, R.; Khorram, M. S.; Halim, M. A.; Khan, M. A. ‘Cordycepin downregulates Cdk2 to interfere with cell cycle and increases apoptosis by generating ROS in cervical cancer cells: in vitro and in silico study’ Current Cancer Drug Target, 2019, 19, 152-159 DOI: 10.2174/1568009618666180905095356 Publisher: Bentham Science, UAE.
(36) Mahbub, S.; Shahriar, I.; Iqfath, M.; Hoque, M. A.; Halim, M. A.; Khan, M. A.; Rub, M. A.; Asiri, A. M. Influence of Alcohols/Electrolytes on the Interaction of Reactive Red Dye with Surfactant and Removal of Dye from Solutions. J. Environ. Chem. Eng. 2019, 7 (5), 103364. https://doi.org/https://doi.org/10.1016/j.jece.2019.103364. Publisher: Elsevier, Netherlands
(35) Shahinozzaman, M.; Ishii, T.; Halim, M. A.; Hossain, M. A.; Islam, M. T.; Tawata, S. Cytotoxic and Anti-Inflammatory Resorcinol and Alkylbenzoquinone Derivatives from the Leaves of Ardisia Sieboldii. Zeitschrift für Naturforschung C. 2019, 74, 303–311. https://doi.org/10.1515/znc-2019-0114. Publisher: DE GRUYTER GmBH, Germany.
2018
(34) Dominguez-Medina, S.; Fostner, S.; Defoort, M.; Sansa, M.; Stark, A. K.; Halim, M. A.; Vernhes, E.; Gely, M.; Jourdan, G.; Alava, T.; Boulanger, P., Masselon, C.; Hentz, S. ‘Neutral Mass Spectrometry of Virus Capsid above 100 MDa with Nanomechnical Resonators’. Science, 2018, 362, 918-922. Publisher: American Association for the Advancement of Science, USA.
(33) *Pansieri, J.; *Halim, M. A.; Vendrely, C.; Dumoulin, M.; Moulin, M.; Chierici, S.; Denti, S.; Dagany, X.; Dugourd, P. ; Marquette, C.; Antoine, R.; Forge, V. “Mass and charge distributions of entire amyloid fibers involved in neurodegenerative diseases : Mapping polymorphism effects and population heterogeneity.” Chemical Science. 2018, 9, 2791-2796. DOI:10.1039/C7SC04542E, Publisher: Royal Society of Chemistry, UK. *Co-first author.
(32) Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “Ultraviolet, Infrared and High-Low Energy Photodissociation of Post-Translationally Modified Peptides.” Journal of American Society for Mass Spectrometry, 2018, 29, 270–283. DOI: 10.1007/s13361-017-1794-9. Publisher: American Society for Mass Spectrometry, USA
(31) Halim, M. A.; Clavier, F.; Dagany, X.; Kerleroux, M.; Dugourd, P.; Dunbar, R.; Antoine, R. “Fragmentation of Single Megadalton Polymer Ions in a Gated Electrostatic Ion Trap. The Added Value of Statistical Analysis of Individual Events.” Physical Chemistry Chemical Physics. 2018, 20, 11959-11966 DOI:10.1039/C8CP00404H, Publisher: Royal Society of Chemistry, UK
(30) Hoque, M. A.; Molla, M.; Rana, S.; Rub, M. A.; Ahmed, F.; Rahman, M.; Halim, M. A. ‘Influence of Salt and Temperature on the Interaction of Bovine Serum Albumin with Cetylpyridinium Chloride: Insights from Experimental and Molecular Dynamics Simulation’. Journal of Molecular Liquids, 2018, 260, 121-130. https://doi.org/10.1016/j.molliq.2018.03.069 Publisher: Elsevier, Netherlands
(29) Shahinozzaman, M.; Ishii, T.; Takano, R.; Halim, M. A.; Hossain, M. A.; Tawata, S. ‘Anti-inflammatory, anti-diabetic and anti-Alzheimer effects of prenylated flavonoids from Okinawa propolis: an investigation by experimental and computational studies’ Molecules, 2018, 23(10), 2479. https://doi.org/10.3390/molecules23102479 Publisher: Multidisciplinary Digital Institute (MPDI), Switzerland.
(28) Eid, E.; Azam, F.; Hassan, M.; Taban, I.; Halim, M. A. ‘Zerumbone binding to estrogen receptors: an in-silico investigation’ Journal of Receptors and Signal Transduction, 2018, 38,342-351. DOI: 10.1080/10799893.2018.1531886. Publisher: Taylor and Francis, UK
(27) Shahinozzaman, M.; Ishii, T.; Takano, R.; Halim, M. A.; Hossain, M. A.; Tawata, S. ‘Cytotoxic desulfated saponin from Holothuria atra shows high binding affinity to the oncogenic kinase PAK1: a combined in vitro and in silico study’ Scientia Pharmaceutica, 2018, 86(3), 32. https://doi.org/10.3390/scipharm86030032. Publisher: Multidisciplinary Digital Institute (MPDI), Switzerland.
(26) Junaid, M.; Alam, M. J.; Hossain, M, K.; Halim, M. A.; Ullah, M. O. ‘Molecular Docking and Dynamics of Nickel-Schiff base Complexes for inhibiting Β-lactamase of Mycobacterium Tuberculosis.’ In Silico Pharmacology, 2018, 6, 1-11. DOI: 10.1007/s40203-018-0044-6 Publisher: Springer, Germany
(25) Hoque, M. A.; Rana, S.; Molla, M. R.; Alam, M. M.; Rub, M. A.; Halim, M. A.; Akhtar, F.; Khan, M. A. “Interaction of cetyltrimethylammonium bromide with drug in aqueous/electrolyte solution: A Conductometric and Molecular Dynamics Method Study’’ Chinese Journal of Chemical Engineering, 2018, 26, 159-167 https://doi.org/10.1016/j.cjche.2017.06.016 Publisher: Elsevier, Netherlands
(24) Shawon, J.; Khan, A. M.; Rahman, A.; Hoque, M. M.; khan, M. A. K.; Sarwar, M. S.; Halim, M. A. ‘Molecular Recognition of Azelaic Acid and Related Molecules with DNA polymerase I Investigated by Molecular Modelling Calculations’ Interdisciplinary Sciences: Computational Life Sciences, 2018, 10, 525–537. doi:10.1007/s12539-016-0186-3. Publisher: Springer, Germany
2017
(23) Daly, S.; Knight, G.; Halim, M. A.; Kulesza, A.; MacAleese, L; Antoine, R.; Dugourd, P. “Action-FRET of a Gaseous Protein” Journal of American Society for Mass Spectrometry 2017, 28, 38-49. doi:10.1007/s13361-016-1449-2. Publisher: American Society for Mass Spectrometry, USA
(22) Hoque, M. A.; Alam, M. M.; Rana, S.; Molla, M. R.; Rub, M. A.; Halim, M. A.; Khan, M. A.;“ Effect of Salts and Temperature on the Interaction of Levofloxacin Hemihydrate Drug with Cetyltrimethylammonium Bromide: A Combined Conductometric and Molecular Dynamics Method Study’’ Journal of Molecular Liquid, 2017, 244, 512-520. https://doi.org/10.1016/j.molliq.2017.09.004. Publisher: Elsevier, Netherlands
(21) Rahman, M. S.; Hossain, S. M.; Rahman, M. T.; Halim, M. A.; Ishtiak, M. N.; Kabir, M. Determination of Trace Metal Concentration in Compost, DAP, and TSP Fertilizers by Neutron Activation Analysis (NAA) and Insights from Density Functional Theory Calculations. Environmental Monitoring and Assessment 2017, 189 (12), 618 DOI: 10.1007/s10661-017-6328-1. Publisher: Springer, Germany
(20) Khan, A.; Shawon, J.; Halim, M. A. “Multiple Receptor Conformers based Molecular Docking study of Fluorine Enhanced Ethionamide with Mycobacterium Enoyl ACP Reductase (InhA)” Journal of Molecular Graphics and Modelling, 2017, 77, 386-398, https://doi.org/10.1016/j.jmgm.2017.09.010 Publisher: Elsevier, Netherlands
(19) Zangrando, E., Begum M. S.; Sheikh, M. C.; Miyatake, R.; Hossain, M. M.; Alam, M. M.; Hasnat, M. A.; Halim, M. A.; Ahmed, S.; Rahman, M. N.; Ghosh, A. “Synthesis, characterization, density functional study and antimicrobial evaluation of a series of bischelated complexes with a dithiocarbazate Schiff base ligand. ” Arabian Journal of Chemistry 2017, 10, 172-184. https://doi.org/10.1016/j.arabjc.2016.07.019 Publisher: Elsevier, Netherlands
(18) Naseem, S., Khalid, M., Tahir, M.N., Halim, M.A., Braga, A.A.C., Naseer, M. M., Shafiq, Z. “Synthesis, structural, DFT studies, docking and antibacterial activity of xanthene based hydrazone ligand.” Journal of Molecular Structure. 2017, 1143, 235–244. https://doi.org/10.1016/j.molstruc.2017.04.093. Publisher: Elsevier, Netherlands
(17) Hoque, M. A.; Patoary, M. O. F.; Molla, M. R.; Halim, M. A.; Khan, M. A.; Rub, M. A.‘Interaction Between Cetylpyridinium Chloride and Amino Acids: A Conductomertic and Computational Method Study’ Journal of Dispersion Science and Technology, 2017, 38, 1578–1587. http://dx.doi.org/10.1080/01932691.2016.1262779. Publisher: Taylor & Francis, UK
(16) Adeel, M.; Braga, A. A. C.; Tahir, M. N.; Haq, F.; Khalid, M.; Halim, M. A. “Synthesis, X-Ray Crystallographic, Spectroscopic and Computational Studies of Aminothiazole Derivatives.” Journal of Molecular Structure 2017, 1131, 136–148.https://doi.org/10.1016/j.molstruc.2016.11.046. Publisher: Elsevier, Netherlands
2016
(15) Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization.” Journal of American Society for Mass Spectrometry 2016, 27, 1435-1442. doi:10.1007/s13361-016-1419-8 (Cover Article) Publisher: American Society for Mass Spectrometry, USA
(14) Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “213 nm Ultraviolet Photodissociation on Peptide Anions: Radical-Directed Fragmentation Patterns.” Journal of American Society for Mass Spectrometry 2016, 27, 474-486. DOI: 10.1007/s13361-015-1297-5. Publisher: American Society for Mass Spectrometry, USA
(13) Rahman, A.; Ali, M. T.; Shawan, M. A. K.; Sarwar, M. G.; Khan, M. A. K. Halim, M. A.*; “Halogen-directed Drug Design for Alzheimer’s disease: A Density Functional and Molecular Docking Study. SpringerPlus, 2016, 5, 1345. DOI: 10.1186/s40064-016-2996-5. Publisher: Springer, Germany
(12) Saleh, M. A.; Solayman, M.; Hoque, M. M.; khan, M. A. K.; Sarwar, M. S.; Halim, M. A. “Inhibition of DNA Topoisomerase Type IIα (TOP2A) by Mitoxantrone and Its Halogenated Derivatives: A Combined Density Functional and Molecular Docking Study.” Biomed Research International 2016, Article ID 6817502, 12 pages. http://dx.doi.org/10.1155/2016/6817502. Publisher: Hindawi, Egypt.
(11) Rahman, A.; Hoque, M. M.; khan, M. A. K.; Sarwar, M. S.; Halim, M. A.* “Non-covalent interactions involving halogenated derivatives of capecitabine and thymidylate synthase: a computational approach.” Springer Plus 2016, 5, 146. DOI: 10.1186/s40064-016-1844-y. Publisher: Springer, Germany
(10) Killoran, R. C.; Sowole, M. A.; Halim, M. A.; Konermann, L.; Choy, W.-Y. “Conformational Characterization of the Intrinsically Disordered Protein Chibby: Interplay between Structural Elements in Target Recognition” Protein Science, 2016, 25, 1420-1429. DOI: 10.1002/pro.2936. Publisher: John Wiley & Sons, USA
2010-2015
(9) Enamullah, M.; Quddus, A.; Islam, M. K.; Halim, M. A.;Vasylyeva, V.; Janiak, C. “Switching from 4+1 to 4+2 zinc coordination number through the methyl group position on the pyridyl ligand in the geometric isomers bis[N-2-(4/6-methyl-pyridyl)salicylaldiminato-k2N,O]zinc(II)” Inorganica Chemica Acta 2015, 427, 103-111. https://doi.org/10.1016/j.ica.2014.11.020. Publisher: Elsevier, Netherlands
(8) Hoque, M. M; Halim, M. A.; Sarwar, M. G.; Khan, M. W. “Palladium (ІІ) chloride catalyzed cyclization of 2-alkynyl-4-substituted-N-ethanoyl aniline: Synthesis, Structural and Mechanistic Study” Journal of Physical Organic Chemistry 2015, 28, 732-742. DOI: 10.1002/poc.3477. Publisher: John Wiley & Sons, USA
(7) Hossain, E. M.; Hasan, M. M.; Halim. M. E.; Ehsan, M. Q.; Halim, M. A.* “Interaction between Transition Metals and Phenylalanine: A Combined Experimental and Computational Study”, Spectrochimica Acta Part A: 2015, 138, 499-508. https://doi.org/10.1016/j.saa.2014.11.084. Publisher: Elsevier, Netherlands
(6) Enamuallah, M.; Islam, M. K.; Halim, M. A.; Janiak, C. “Syntheses, spectroscopy, thermal analysis, cyclovoltammetry, X-ray, and TD-DFT analyses on Rh(η4-cod)-enantiopure aminocarboxylate complexes” Journal of Molecular Structure 2015, 1099, 154-162. DOI:10.1016/j.molstruc.2015.06.040. Publisher: Elsevier, Netherlands
(5) Halim, M. A.; Almatarneh, M. H.; Poirier, R. A. “Mechanistic Study of the Deamidation of Glutamine: A Computational Approach” Journal of Physical Chemistry B 2014, 118, 2316-2330. DOI: 10.1021/jp4107266. Publisher: American Chemical Society, USA.
(4) Goni, M. A.; Ahmad, J. U.; Halim, M. A.; Mottalib, M. A.; Chowdhury, D. A. “Uptake and Translocation of Metals in Different Parts of Crop Plants Irrigated with Contaminated Water from DEPZ Area of Bangladesh.” Bulletin of Environmental Contamination Toxicology 2014, 92, 726-732. doi:10.1007/s00128-014-1264-z. Publisher: Springer, Germany
(3) Halim, M.A. ‘Harnessing Sun’s Energy with Quantum Dots Based Next Generation Solar Cell.’ Nanomaterials 2013, 3, 22-47. Publisher: Multidisciplinary Digital Institute (MPDI), Switzerland.
(2) Hoque, M. M.; Halim, M. A.; Rahman, M. M.; Hossain, M. I.; Khan, M. W. “Synthesis and Structural Insights of Substituted 2-iodoacetanilides and 2-iodoanilines”, Journal of Molecular Structure, 2013, 1054-1055, 364-374. https://doi.org/10.1016/j.molstruc.2013.10.011. Publisher: Elsevier, Netherlands
(1) Halim, M. A.; Shaw, D. M.; Poirier, R. A. “Medium Effect on the Equilibrium Geometries, Vibrational Frequencies and Solvation Energies of Sulfanilamide”, Journal of Molecular Structure: THEOCHEM, 2010, 960, 63-72. https://doi.org/10.1016/j.theochem.2010.08.027. Publisher: Elsevier, Netherlands
Dominguez-Medina, S.; Fostner, S.; Defoort, M.; Sansa, M.; Stark, A. K.; Halim, M. A.; Vernhes, E.; Gely, M.; Jourdan, G.; Alava, T.; Boulanger, P., Masselon, C.; Hentz, S. ‘Neutral Mass Spectrometry of Virus Capsid above 100 MDa with Nanomechnical Resonators’. Science, 2018, 362, 918-922. Publisher: American Association for the Advancement of Science, USA.
Featured in Chemistry World: Mass spec goes massive weighing huge virus particles https://bit.ly/2PacJ0G
*Pansieri, J.; *Halim, M. A.; Vendrely, C.; Dumoulin, M.; Moulin, M.; Chierici, S.; Denti, S.; Dagany, X.; Dugourd, P. ; Marquette, C.; Antoine, R.; Forge, V. “Mass and charge distributions of entire amyloid fibers involved in neurodegenerative diseases : Mapping polymorphism effects and population heterogeneity.” Chemical Science. 2018, 9, 2791-2796. DOI:10.1039/C7SC04542E, Publisher: Royal Society of Chemistry, UK. *Co-first author.
Featured in Chemical & Engineering News (C&CN): Charge detection mass spectrometry measures molecular structures too big for regular mass spec, https://bit.ly/2QAtYwo
Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization.” Journal of American Society for Mass Spectrometry 2016, 27, 1435-1442. doi:10.1007/s13361-016-1419-8 (Cover Article) Publisher: American Society for Mass Spectrometry, USA
Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “Ultraviolet, Infrared and High-Low Energy Photodissociation of Post-Translationally Modified Peptides.” Journal of American Society for Mass Spectrometry, 2018, 29, 270–283. DOI: 10.1007/s13361-017-1794-9. Publisher: American Society for Mass Spectrometry, USA
Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “213 nm Ultraviolet Photodissociation on Peptide Anions: Radical-Directed Fragmentation Patterns.” Journal of American Society for Mass Spectrometry 2016, 27, 474-486. DOI: 10.1007/s13361-015-1297-5. Publisher: American Society for Mass Spectrometry, USA
Halim, M. A.; Clavier, F.; Dagany, X.; Kerleroux, M.; Dugourd, P.; Dunbar, R.; Antoine, R. “Fragmentation of Single Megadalton Polymer Ions in a Gated Electrostatic Ion Trap. The Added Value of Statistical Analysis of Individual Events.” Physical Chemistry Chemical Physics. 2018, 20, 11959-11966 DOI:10.1039/C8CP00404H, Publisher: Royal Society of Chemistry, UK
Halim, M. A.; Bertorelle, F.; Doussineau, T.; and Antoine, R. ‘Direct Molecular Weight Distribution of Calf-Thymus DNAs and Fragmentation under Ultrasonic and Low-Energy IR Irradiations. A Charge Detection Mass Spectrometry Investigation.’ Rapid Communication in Mass Spectrometry, 2019, 33 (S1), 35-39. https://doi.org/10.1002/rcm.8204. Publisher: John Wiley & Sons, USA
2023
(95) Stewart, J.; Shawon, J.; Ali, M. A.; Shahinuzzaman, A.; Rupa, S.; Williams, B.; Al-Adhami, T.; Jia, Bourque, C.; R.; Faddis, R.; Stone, K.; Sufian, M. A.; Islam, R.; McShan, A. C.; Rahman, K. M.; Halim, M. A. Antiviral Peptides Inhibiting the Main Protease of SARS-CoV-2 Investigated by Computational Screening and In-Vitro Protease Assay. Journal of Peptide Science 2023. Accepted.
(94) Faddis, R.; Du, S.; Stewart, J.; Hasan, M. M.; Lewit. N. Ali, M. A.; White, C. B.; Okoto, P.; Thallapuranam, S.; Halim, M. A. 'Molecular Modelling, Synthesis, and In-Vitro Assay to Identify Potential Antiviral Peptides targeting the 3-Chymotrypsin-like Protease of SARS-CoV-2' International Journal of Peptide Research and Therapeutics, 2023, 29, 89 https://doi.org/10.1007/s10989-023-10563-w
(93) Rub, M. A.; Azum, N.; Alfaifi, S. Y. M.; Sakib, M. M. H., Ali, M. A.; Mahbub, S.; Haim, M. A.; Hoque, M. A.; Asiri, A. M.
'Assessment of mixed micellization behavior of amitriptyline hydrochloride and TX-165 surfactant mixture in various media (aqueous/NaCl/urea)', Journal of Molecular Liquids, 2023, In press. https://doi.org/10.1016/j.molliq.2023.122073 Publisher: Elsevier, Netherlands.
(92) Ali, M. A.; Kaium, M. A.; Uddin, S. N.; Uddin, M. J.; Olawuyi, O.; Campbell, A. D. Jr.; Saint-Louis, C. J.; Halim, M. A. Elucidating the Structure, Dynamics, and Interaction of a Choline Chloride and Citric Acid Based Eutectic System by Spectroscopic and Molecular Modeling Investigations. ACS Omega 2023. https://doi.org/10.1021/acsomega.3c04570
(91) Akter, S.; Islam, M. J.; Ali, M. A.; Tashrif, M. Z.; Uddin, M. J.; Ullah, M. O.; Halim, M. A. 'Structure and dynamics of whole-sequence homology model of ORF3a protein of SARS-CoV-2: An insight from microsecond molecular dynamics simulations', Journal of Biomolecular Structure and Dynamics, 2023, DOI: 10.1080/07391102.2023.2236715, Publisher: Taylor and Francis, UK
(90) Uddin, M. J.; Akhter, H.; Chowdhury, U.; Mawah, J.; Karim, S. T.; Jomel, M.; Islam, M. S.; Islam, M. R.; Onin, L. A. B.; Ali, Halim, M. A. Large Scale Peptide Screening against Main Protease of SARS CoV‐2. Journal of Computational Chemistry 2023, 44(8), 869-947. https://doi.org/10.1002/jcc.27050. Publisher: John Wiley & Sons, USA
(89) Hossain, Md. S.; Shovon, Md. T. I.; Hasan, Md. R.; Hakim, F. T.; Hasan, M. M.; Esha, S. A.; Tasnim, S.; Nazir, Md. S.; Akhter, F.; Ali, M. A.; Halim, M. A. Therapeutic Potential of Antiviral Peptides against the NS2B/NS3 Protease of Zika Virus. ACS Omega 2023, 8 (38), 35207–35218. https://doi.org/10.1021/acsomega.3c04903.
(88) Islam, S.; Parves, M. R.; Islam, M. J.; Ali, M. A.; Efaz, F. M.; Hossain, M. S.; Ullah, M. O.; Halim, M. A. 'Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study' Journal of Biomolecular Structure and Dynamics 2023. https://doi.org/10.1080/07391102.2023.2228919 Publisher: Taylor and Francis, UK
(87) Islam, M. J.; Islam, N. N.; Alom, M. S.; Kabir, M.; Halim, M. A. 'A Review on Structural, Non-Structural, and Accessory Proteins of SARS-CoV-2: Highlighting Drug Target Sites'. Immunobiology 2023, 152302. Publisher: Elsevier, Netherlands.
(86) Hossen, M. R.; Biswas, S.; Ali, M. A.; Halim, M. A.; Ullah, M. O. 'In silico peptide-based therapeutics against human colorectal cancer by the activation of TLR5 signaling pathways', Journal of Molecular Modelling, 2023, 29, 35. Publisher: Springer
(85) Biswas, B.; Hossen, M. R.; Akter, S.; Ali, M. A., Halim, M. A.; Ullah, M. O. ‘Structural dynamics and functional analysis of Saprolegnia parasitica chitin synthases 5 in a phospholipid bilayer’, Journal of Biomolecular Structure and Dynamics 2023. DOI: 10.1080/07391102.2023.2193993 Publisher: Taylor and Francis, UK
2022
(84) Jiang, L. X.; Plath, L. D.; Halim, M. A.; Friedrich, S.; Bier, M. E. 'Anatomy of Protein Electrospray Ionization Mass Spectra by Superconducting Tunnel Junction Mass and Energy Spectrometry' Analytical Chemistry 2022, 94 (13), 5284-5292 DOI: 10.1021/acs.analchem.1c05074 Publisher: American Chemical Society, USA.
(83) Rahman, M. S.; Roy, R.; Montoya, C.; Halim, M. A.; Raynie, D. E. Acidic and Basic Amino Acid-Based Novel Deep Eutectic Solvents and Their Role in Depolymerization of Lignin. Journal of Molecular Liquids 2022, 362, 119751. https://doi.org/https://doi.org/10.1016/j.molliq.2022.119751. Publisher: Elsevier, Netherlands.
(82) Raha, F. K.; Hasan, J.; Ali, M. A.; Fakayode, S. O.; Halim, M. A. Exploring the molecular level interaction of Xenoestrogen phthalate plasticisers with oestrogen receptor alpha (ERα) Y537S mutant, Molecular Simulation, 2022, DOI: 10.1080/08927022.2022.2101675 Publisher: Taylor & Francis, UK
(81) Mahdi, I.; Yeasmin, H.; Hossain, I.; Badhan, R. M.; Ali, M. A.; Kaium, M.; Islam, R.; Sufian, M.; Halim, M. A., Potential antiviral peptides against the nucleoprotein of SARS-CoV-2, Chemical Paper, 2022, In press, https://link.springer.com/article/10.1007/s11696-022-02514-4 Publisher: Springer
(80) Hasan, M. M.; Shahriar, I.; Ali, M. A.; Halim, M. A.; Ehsan, Q. M. Experimental and computational studies on transition metals interaction with Leucine and Isoleucine, Journal of Molecular Structure, 2022, 1270, 133862. https://doi.org/10.1016/j.molstruc.2022.133862 Publisher: Elsevier, Netherlands.
(79) Zohora, F. T.; Azam, A. T. M.; Ahmed, S.; Rahman, K. M.; Halim, M. A.; Anwar, M.; Sohrab, M.; Tabassum, F.; Hasan, C. M.; Ahsan, M. Isolation and In Silico Prediction of Potential Drug-like Compounds with a New Dimeric Prenylated Quinolone Alkaloid from Zanthoxylum Rhetsa (Roxb.) Root Extracts Targeted against SARS-CoV-2 (Mpro). Molecules 2022, 27 (23), 8191
(78) Uddin, M. J.; Faraone, I.; Haque, M. A.; Rahman, M. M.; Halim, M. A.; Sönnichsen, F. D.; Çiçek, S. S.; Milella, L.; Zidorn, C. Insights into the leaves of Ceriscoides campanulata: Natural proanthocyanidins alleviate diabetes, inflammation, and esophageal squamous cell cancer via in vitro and in silico models, Fitoterapia, 2022, 158, 105164, https://doi.org/10.1016/j.fitote.2022.105164. Publisher: Elsevier, Netherlands.
(77) Rahman, M. S.; Kyeremateng, J.; Saha, M.; Asare, S.; Uddin, N.; Halim, M. A.; Raynie, D. E. Evaluation of the experimental and computed properties of choline chloride-water formulated deep eutectic solvents, Journal of Molecular Liquids 2022, 350, 118520. https://doi.org/10.1016/j.molliq.2022.118520. Publisher: Elsevier, Netherlands.
(76) Haque, M. A; Islam, K. B.; Mahbub, S.; Masood Khan, J.; Hossian, J.; Anamul Hoque, M.; Halim, M. A.; Majibur Rahman, M.; Ahmad, A.; Ahmed, M. Z. Impact of Ethanol and NaCl on the Acid Yellow Dye Mediated Self-Aggregation of Sodium Dodecyl Sulfate: A Combined Investigation by Conductivity and Molecular Dynamics Simulation. Journal of Molecular Liquids 2022, 345, 117819. https://doi.org/https://doi.org/10.1016/j.molliq.2021.117819 Publisher: Elsevier, Netherlands.
(75) Omor Faruk Patwary, M.; Mahbubur Rahman, M.; Khalid Bin Islam, M.; Ackas Ali, M.; Halim, M. A.; Ahmed, F. 'Probing the Non-Bonding Interaction of Small Molecules with Graphene Oxide Using DFT Based Vibrational Circular Dichroism.' Computational and Theoretical Chemistry 2022, 1207, 113503. 8 https://doi.org/https://doi.org/10.1016/j.comptc.2021.113503. Publisher: Elsevier, Netherlands.
(74) Khan, A. T.; Chowdhury, G. M.; Hafsah, J.; Maruf, M.; Raihan, M. R. H.; Chowdhury, M. T.; Nawal, N.; Tasnim, N.; Saha, P.; Roy, P.; Tabassum, R.; Rodrigues, S. P.; Hasan, W.; Samanta, Z. T.; Kamal, S.; Nazir, M. S.; Ali, M. A.; Halim, M. A.* A Student Led Computational Screening of Peptide Inhibitors against Main Protease of SARS-CoV-2. Biochemistry and Molecular Biology Education 2022, 50, 7-20. https://doi.org/https://doi.org/10.1002/bmb.21580. Publisher: John Wiley & Sons, USA
(73) Sultana, M. U. C.; Uddin, M. G.; Hossain, M. B.; Ali, M. A.; Sonia, Z. F.; Kamal, S.; Halim, M. A.* Molecular Dynamics Investigation of Ivermectin Bound to Importin Alpha/Beta Heterodimer. Molecular Simulation 2022, 48, 314-321. https://doi.org/10.1080/08927022.2021.2015066. Publisher: Taylor & Francis, UK
2021
(72) Efaz, F. Md.; Islam, S.; Talukder, S. A.; Akter, S.; Tashrif, Md. Z.; Ali, Md. A.; Sufian, Md. A.; Parves, Md. R.; Islam, Md. J.; Halim, M. A.* Repurposing Fusion Inhibitor Peptide against SARS-CoV-2. Journal of Computational Chemistry 2021, 42, 2283-2293. https://doi.org/https://doi.org/10.1002/jcc.26758. Publisher: John Wiley & Sons, USA
(71) Rain, M. I.; Iqbal, H.; Saha, M.; Ali, M. A.; Chohan, H. K.; Rahman, M. S.; Halim, M. A. A Comprehensive Computational and Principal Component Analysis on Various Choline Chloride-Based Deep Eutectic Solvents to Reveal Their Structural and Spectroscopic Properties. Journal of Chemical Physics 2021, 155 (4), 44308. https://doi.org/10.1063/5.0052569. Publisher: American Institute of Physics (AIP), USA.
(70) Hossain Sakib, M. M.; Nishat, A. A.; Islam, M. T.; Raihan Uddin, M. A.; Iqbal, M. S.; Bin Hossen, F. F.; Ahmed, M. I.; Bashir, M. S.; Hossain, T.; Tohura, U. S.; Saif, S. I.; Jui, N. R.; Alam, M.; Islam, M. A.; Hasan, M. M.; Sufian, M. A.; Ali, M. A.; Islam, R.; Hossain, M. A.; Halim, M. A. Computational Screening of 645 Antiviral Peptides Against the Receptor-Binding Domain of the Spike Protein in SARS-CoV-2. Computers in Biology and Medicine 2021, 136, 104759. https://doi.org/10.1016/j.compbiomed.2021.104759. Publisher: Elsevier, Netherlands
(69) Ali, M. A.; Rahman, M. S.; Roy, R.; Gambill, P.; Raynie, D. E.; Halim, M. A. Structure Elucidation of Menthol-Based Deep Eutectic Solvent Using Experimental and Computational Techniques. Journal of Physical Chemistry A 2021, 125 (12), 2402–2412. https://doi.org/10.1021/acs.jpca.0c10735. Publisher: American Chemical Society, USA.
(68) Khan, A. T.; Chowdhury, G. M.; Hafsah, J.; Maruf, M.; Raihan, M. R. H.; Chowdhury, M. T.; Nawal, N.; Tasnim, N.; Saha, P.; Roy, P.; Tabassum, R.; Rodrigues, S. P.; Hasan, W.; Samanta, Z. T.; Kamal, S.; Nazir, M. S.; Ali, M. A.; Halim, M. A. A Student Led Computational Screening of Peptide Inhibitors against Main Protease of SARS-CoV-2. Biochemistry and Molecular Biology Education 2021, n/a (n/a). https://doi.org/https://doi.org/10.1002/bmb.21580.
(67) Uddin, M. J.; Russo, D.; Rahman, M. M.; Uddin, S. B.; Halim, M. A.; Zidorn, C.; Milella, L.Anticholinesterase Activity of Eight Medicinal Plant Species: In Vitro and In Silico Studies in the Search for Therapeutic Agents against Alzheimer’s Disease. Evidence-Based Complement. Altern. Med. 2021, 2021, 9995614. https://doi.org/10.1155/2021/9995614. Publisher: Hindawi, Egypt.
(66) Khan, M. T.; Islam, M. J.; Parihar, A.; Islam, R.; Jerin, T. J.; Dhote, R.; Ali, M. A.; Laura, F. K.; Halim, M. A. Immunoinformatics and Molecular Modeling Approach to Design Universal Multi-Epitope Vaccine for SARS-CoV-2. Informatics Med. Unlocked 2021, 100578. https://doi.org/https://doi.org/10.1016/j.imu.2021.100578. Publisher: Elsevier, Netherlands
(65) Mamun, A. al; Akter, F.; Khan, M.; Ahmed, S. S.; Uddin, Md. G.; Tasfia, N. T.; Efaz, F. Md.; Ali, M. A.; Sultana, M. U. C.; Halim, M. A. Identification of Potent Inhibitors against Transmembrane Serine Protease 2 for Developing Therapeutics against SARS-CoV-2. Journal of Biomolecular Structure and Dynamics 2021, 1–13. https://doi.org/10.1080/07391102.2021.1980109. Publisher: Taylor and Francis, UK
(64) Rahman, M. S.; Roy, R.; Jadhav, B.; Hossain, M. N.; Halim, M. A.; Raynie, D. E. Formulation, Structure, and Applications of Therapeutic and Amino Acid-Based Deep Eutectic Solvents: An Overview. Journal of Molecular Liquids 2021, 321,114745. https://doi.org/https://doi.org/10.1016/j.molliq.2020.114745. Publisher: Elsevier, Netherlands
(63) Rahman, M. M.; Biswas, S.; Islam, K. J.; Paul, A. S.; Mahato, S. K.; Ali, M. A.; Halim, M. A. Antiviral Phytochemicals as Potent Inhibitors against NS3 Protease of Dengue Virus. Computers in Biology and Medicine 2021, 134, 104492. https://doi.org/https://doi.org/10.1016/j.compbiomed.2021.104492. Publisher: Elsevier, Netherlands
(62) Mahmud, S.; Islam, M. J.; Parves, M. R.; Khan, M. A.; Tabussum, L.; Ahmed, S.; Ali, M. A.; Fakayode, S. O.; Halim, M. A. Designing Potent Inhibitors against the Multidrug Resistance P-Glycoprotein. Journal of Biomolecular Structure & Dynamics, 2021. In press, https://doi.org/10.1080/07391102.2021.1930159.Publisher: Taylor and Francis, UK
(61) Rahim, M. A.; Mahbub, S.; Ahsan, S. M. A.; Manawwer, A.; Saha, M.; Shahriar, I.; Rana, S.; Halim, M. A.; Hoque, M. A.; Kumar, D.; Khan, J. M.; ‘Conductivity, cloud point and molecular dynamics investigations of the interaction of surfactants with ciprofloxacin hydrochloride drug: Effect of electrolytes’ Journal of Molecular Liquids, 2021, 322, 114683. https://doi.org/10.1016/j.molliq.2020.114683 Publisher: Elsevier, Netherlands
(60) Shawon, J.; Khan, A. M.; Shahriar, I.; Halim, M. A. Improving the Binding Affinity and Interaction of 5-Pentyl-2-Phenoxyphenol against Mycobacterium Enoyl ACP Reductase by Computational Approach. Informatics Med. Unlocked 2021, 23, 100528. https://doi.org/10.1016/j.imu.2021.100528. Publisher: Elsevier, Netherlands
(59) Islam, R.; Parves, R.; Paul, A. S.; Uddin, N.; Rahman, M. S.; Mamun, A. Al; Hossain, M. N.; Ali, M. A.; Halim, M. A. ‘A Molecular Modeling Approach to Identify Effective Antiviral Phytochemicals against the Main Protease of SARS-CoV-2.’ Journal of Biomolecular Structure & Dynamics 2021, 39 (9), 3213-3224. https://doi.org/10.1080/07391102.2020.1761883. Publisher: Taylor and Francis, UK
(58) Zahan, R.; Ahmed, S.; Sharmin, T.; Halim, M. A.; Rahi, M. S.; Sheikh, M. C.; Miyatake, R.; Zangrando, E.; Naz, T.; Islam, M. A.-A.-A.-A.; Reza, M. A. Synthesis of Bis[Benzyl-N′-Hydrazinecarbodithioato-Κ2 N′,S]Nickel(II) Complex as a Novel Lead Molecule for Cancer Treatment. Appl. Organomet. Chem. 2021, 35(1), e6036. https://doi.org/10.1002/aoc.6036. Publisher: John Wiley & Sons, USA
2020
(57) Chowdhury, S. M.; Talukder, S. A.; Khan, A. M.; Afrin, N.; Ali, M. A.; Islam, R.; Parves, R.; Mamun, A. A.; Sufian, M. A.; Hossain, M. N.; Hossain, M. A.; Halim, M. A. ‘Antiviral Peptides as Promising Therapeutics against SARS-CoV-2’ Journal of Physical Chemistry B, 2020, 124, 9785-9792. https://doi.org/10.1021/acs.jpcb.0c05621 Publisher: American Chemical Society, USA.
(56) Saha, M.; Rahman, M. S; Hossain, M. N.; Raynie, D. E.; Halim, M. A.; ‘Molecular and Spectroscopic Insights of a Choline Chloride Based Therapeutic Deep Eutectic Solvent’ 2020, 124, 4690–4699. The Journal of Physical Chemistry A, DOI: 10.1021/acs.jpca.0c00851 Publisher: American Chemical Society, USA
(55) Paul, A. S.; Islam, R.; Parves, R.; Mamun, A. Al; Shahriar, I.; Hossain, M. I.; Hossain, M. N.; Ali, M. A.; Halim, M. A. ‘Cysteine focused covalent inhibitors against the main protease of SARS-CoV-2.’ Journal of Biomolecular Structure & Dynamics 2020, 1-20. In press, DOI: 10.1080/07391102.2020.1831610 Publisher: Taylor and Francis, UK
(54) Almatarneh, M.H.; Alnajajrah, A.; Altarawneh, M.; Zhao, Y.; Halim, M. A. Computational mechanistic study of the unimolecular dissociation of ethyl hydroperoxide and its bimolecular reactions with atmospheric species. Scientific Report 2020, 10, 15025. https://doi.org/10.1038/s41598-020-71881-3 Publisher: Nature Publishing Group, UK.
(53) Mahtarin, R.; Islam, S.; Islam, M. J.; Ullah, M. U.; Ali, M. A.; Halim, M. A. Structure and dynamics of membrane protein in SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 2020, 1-14, In press DOI: 10.1080/07391102.2020.1861983 Publisher: Taylor and Francis, UK
(52) Ahmed, S.; Mahtarin, R.; Ahmed, S. S.; Akter, S.; Islam, M. S.; Mamun, A. Al; Islam, R.; Hossain, M. N.; Ali, M. A.; Sultana, M. U. C.; Halim, M. A. Investigating the Binding Affinity, Interaction, and Structure-Activity-Relationship of 76 Prescription Antiviral Drugs Targeting RdRp and Mpro of SARS-CoV-2. Journal of Biomolecular Structure & Dynamics 2020, 1–16. https://doi.org/10.1080/07391102.2020.1796804 Publisher: Taylor and Francis, UK
(51) Rahman, M. M.; Saha, T.; Islam, K. J.; Suman, R. H.; Biswas, S.; Rahat, E. U.; Hossen, M. R.; Islam, R.; Hossain, M. N.; Mamun, A. Al; Ackas, M.; Halim, M. A. Virtual Screening, Molecular Dynamics and Structure--Activity Relationship Studies to Identify Potent Approved Drugs for Covid-19 Treatment. Journal of Biomolecular Structure & Dynamics. 2020, 1–11. https://doi.org/10.1080/07391102.2020.1794974 Publisher: Taylor and Francis, UK
(50) Ahmed, S.; Islam, N.; Shahinozzaman, M.; Fakayode, S. O.; Afrin, N.; Halim, M. A. ‘Virtual Screening, Molecular Dynamics, Density Functional Theory and Quantitative Structure Activity Relationship Studies to Design Peroxisome Proliferator-Activated Receptor-γ Agonists as Anti-Diabetic Drugs’ Journal of Biomolecular Structure & Dynamics 2020, 1–15. https://doi.org/10.1080/07391102.2020.1714482. Publisher: Taylor and Francis, UK
(49) Amin, M. R.; Alissa, S. A.; Saha, M.; Hossian, J.; Shahriar, I.; Halim, M. A.; Hoque, M. A.; Alothman, Z. A.; Wabaidur, S. M.; Kabir, S. E. ‘Investigation of the Impacts of Temperature and Electrolyte on the Interaction of Cationic Surfactant with Promethazine Hydrochloride: Combined Conductivity and Molecular Dynamics Studies.’ Journal of Molecular Liquids 2020, 113246. https://doi.org/10.1016/j.molliq.2020.113246. Publisher: Elsevier, Netherlands
(48) Aktar, S.; Saha, M.; Mahbub, S.; Halim, M. A.; Rub, M. A.; Hoque, M. A.; Islam, D. M. S.; Kumar, D.; Alghamdi, Y. G.; Asiri, A. M. ‘Influence of Polyethylene Glycol on the Aggregation/Clouding Phenomena of Cationic and Non-Ionic Surfactants in Attendance of Electrolytes (NaCl & Na2SO4): An Experimental and Theoretical Analysis.’ Journal of Molecular Liquids 2020, 306, 112880. https://doi.org/https://doi.org/10.1016/j.molliq.2020.112880. Publisher: Elsevier, Netherlands
(47) Nasreen, W.; Sarker, S.; Sufian, M. A.; Opo, F. A. D. M.; Shahriar, M.; Akhter, R.; Halim, M. A. ‘A Possible Alternative Therapy for Type 2 Diabetes Using Myristica Fragrans Houtt in Combination with Glimepiride: In Vivo Evaluation and in Silico Support.’ Zeitschrift für Naturforsch. C 2020, 75 (3–4), 103–112. https://doi.org/https://doi.org/10.1515/znc-2019-0134. Publisher: DE GRUYTER GmBH, Germany.
(46) Shahinozzaman, M.; Ishii, T.; Ahmed, S.; Halim, M. A.; Tawata, S. ‘A Computational Approach to Explore and Identify Potential Herbal Inhibitors for the P21-Activated Kinase 1 (PAK1).’ Journal of Biomolecular Structure & Dynamics 2020, 38 (12), 3514-3526. https://doi.org/10.1080/07391102.2019.1659855. Publisher: Taylor and Francis, UK
(45) Uddin, N.; Ahmed, S.; khan, M. A. K.; Hoque, M. M.; Halim, M. A. ‘Halogenated Derivatives of Methotrexate as Human Dihydrofolate Reductase Inhibitor in Cancer Chemotherapy’ the Journal of Biomolecular Structure & Dynamics, 2020. 38 (3), 901-917. https://doi.org/10.1080/07391102.2019.1591302 Publisher: Taylor and Francis, UK
2019
(44) Halim, M. A.; Bertorelle, F.; Doussineau, T.; and Antoine, R. ‘Direct Molecular Weight Distribution of Calf-Thymus DNAs and Fragmentation under Ultrasonic and Low-Energy IR Irradiations. A Charge Detection Mass Spectrometry Investigation.’ Rapid Communication in Mass Spectrometry, 2019, 33 (S1), 35-39. https://doi.org/10.1002/rcm.8204. Publisher: John Wiley & Sons, USA
(43) Islam, J.; Khan, A. M.; Parves, R. Halim, M. A. "Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking and Molecular Dynamics Simulation" Scientific Report, 2019, 9, 16426. DOI: 10.1038/s41598-019-52308-0. Publisher: Nature Publishing Group, UK.
(42) Junaid, M.; Alam, M. J.; Hossain, M, K.; Ullah, M. O.; Halim, M. A. ‘Metal Based Donepezil Analogues Designed to Inhibit Human Acetylcholinesterase for Alzheimer's disease.’ PLOS ONE, 2019, 14(2): e0211935 https://doi.org/10.1371/journal.pone.0211935 Publisher: Public Library of Science, California, USA.
(41) Ahmed, F.; Molla, M. R.; Shahriar, I.; Saha, M.; Rahman, M. S.; Hoque, M. A.; Halim, M. A.; Rub, M. A.; Asiri A. M.; ‘Aggregation Behavior of Cetyldimethylethylammonium Bromide under the Influence of Bovine Serum Albumin in Aqueous/ Electrolyte Solutions at Various Temperatures and Compositions: Conductivity and Molecular Dynamics Study’, RSC Advances, 2019, 9, 6556-6567. DOI: 10.1039/C9RA00070D. Publisher: Royal Society of Chemistry, UK.
(40) Shahriar, I.; Iqfath, M.; Islam, K. B.; Rahman, A.; Halim, M. A.* “Solvent Effect on Vibrational Circular Dichroism of Chiral Amino Acids” Theoretical Chemistry Accounts, 2019, 138, 32. https://doi.org/10.1007/s00214-019-2419-0 Publisher: Springer, Germany
(39) Mahbub, S.; Shahriar, I.; Saha, M.; Molla, M. R.; Halim, M. A.; Hoque, M. A.; Rub, M. A.; ‘Conductometric and Molecular Dynamics studies of the Aggregation behavior of sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB) in aqueous and electrolytes solution’ Journal of Molecular Liquids, 2019, 283, 263-275. https://doi.org/10.1016/j.molliq.2019.03.045 Publisher: Elsevier, Netherlands
(38) Begum, N.; Islam, M. T.; Hossain, S. R.; Bhuyan, G. S.; Halim, M. A.; Shahriar, I.; Sarker, S. K.; Rahat, A.; Haque, S.; Konika, T. K; Qadri, S. K.; Islam, M. S.; Sultana, R.; Begum, S.; Sultana, S.; Saha, N.; Hasan, M.; Hasanat, M. A.; Banu, H.; Shekhar, H. U.; Chowdhury, E. K.; Sajib, A. A.; Islam, A.; Qadri, S. S.; Qadri, F.; Akhteruzzaman, S.; Mannoor, K. “Mutation spectrum in TPO gene of Bangladeshi patients with thyroid dyshormonogenesis and analysis of the effects of different mutations on the structural features and functions of TPO protein through in silico approach” BioMed Research International, 2019, Article ID 9218903, 1-18. https://doi.org/10.1155/2019/9218903. Publisher: Hindawi, Egypt.
(37) Tania, M.; Shawon, J.; Saif, K.; Rudolf Kiefer, R.; Khorram, M. S.; Halim, M. A.; Khan, M. A. ‘Cordycepin downregulates Cdk2 to interfere with cell cycle and increases apoptosis by generating ROS in cervical cancer cells: in vitro and in silico study’ Current Cancer Drug Target, 2019, 19, 152-159 DOI: 10.2174/1568009618666180905095356 Publisher: Bentham Science, UAE.
(36) Mahbub, S.; Shahriar, I.; Iqfath, M.; Hoque, M. A.; Halim, M. A.; Khan, M. A.; Rub, M. A.; Asiri, A. M. Influence of Alcohols/Electrolytes on the Interaction of Reactive Red Dye with Surfactant and Removal of Dye from Solutions. J. Environ. Chem. Eng. 2019, 7 (5), 103364. https://doi.org/https://doi.org/10.1016/j.jece.2019.103364. Publisher: Elsevier, Netherlands
(35) Shahinozzaman, M.; Ishii, T.; Halim, M. A.; Hossain, M. A.; Islam, M. T.; Tawata, S. Cytotoxic and Anti-Inflammatory Resorcinol and Alkylbenzoquinone Derivatives from the Leaves of Ardisia Sieboldii. Zeitschrift für Naturforschung C. 2019, 74, 303–311. https://doi.org/10.1515/znc-2019-0114. Publisher: DE GRUYTER GmBH, Germany.
2018
(34) Dominguez-Medina, S.; Fostner, S.; Defoort, M.; Sansa, M.; Stark, A. K.; Halim, M. A.; Vernhes, E.; Gely, M.; Jourdan, G.; Alava, T.; Boulanger, P., Masselon, C.; Hentz, S. ‘Neutral Mass Spectrometry of Virus Capsid above 100 MDa with Nanomechnical Resonators’. Science, 2018, 362, 918-922. Publisher: American Association for the Advancement of Science, USA.
(33) *Pansieri, J.; *Halim, M. A.; Vendrely, C.; Dumoulin, M.; Moulin, M.; Chierici, S.; Denti, S.; Dagany, X.; Dugourd, P. ; Marquette, C.; Antoine, R.; Forge, V. “Mass and charge distributions of entire amyloid fibers involved in neurodegenerative diseases : Mapping polymorphism effects and population heterogeneity.” Chemical Science. 2018, 9, 2791-2796. DOI:10.1039/C7SC04542E, Publisher: Royal Society of Chemistry, UK. *Co-first author.
(32) Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “Ultraviolet, Infrared and High-Low Energy Photodissociation of Post-Translationally Modified Peptides.” Journal of American Society for Mass Spectrometry, 2018, 29, 270–283. DOI: 10.1007/s13361-017-1794-9. Publisher: American Society for Mass Spectrometry, USA
(31) Halim, M. A.; Clavier, F.; Dagany, X.; Kerleroux, M.; Dugourd, P.; Dunbar, R.; Antoine, R. “Fragmentation of Single Megadalton Polymer Ions in a Gated Electrostatic Ion Trap. The Added Value of Statistical Analysis of Individual Events.” Physical Chemistry Chemical Physics. 2018, 20, 11959-11966 DOI:10.1039/C8CP00404H, Publisher: Royal Society of Chemistry, UK
(30) Hoque, M. A.; Molla, M.; Rana, S.; Rub, M. A.; Ahmed, F.; Rahman, M.; Halim, M. A. ‘Influence of Salt and Temperature on the Interaction of Bovine Serum Albumin with Cetylpyridinium Chloride: Insights from Experimental and Molecular Dynamics Simulation’. Journal of Molecular Liquids, 2018, 260, 121-130. https://doi.org/10.1016/j.molliq.2018.03.069 Publisher: Elsevier, Netherlands
(29) Shahinozzaman, M.; Ishii, T.; Takano, R.; Halim, M. A.; Hossain, M. A.; Tawata, S. ‘Anti-inflammatory, anti-diabetic and anti-Alzheimer effects of prenylated flavonoids from Okinawa propolis: an investigation by experimental and computational studies’ Molecules, 2018, 23(10), 2479. https://doi.org/10.3390/molecules23102479 Publisher: Multidisciplinary Digital Institute (MPDI), Switzerland.
(28) Eid, E.; Azam, F.; Hassan, M.; Taban, I.; Halim, M. A. ‘Zerumbone binding to estrogen receptors: an in-silico investigation’ Journal of Receptors and Signal Transduction, 2018, 38,342-351. DOI: 10.1080/10799893.2018.1531886. Publisher: Taylor and Francis, UK
(27) Shahinozzaman, M.; Ishii, T.; Takano, R.; Halim, M. A.; Hossain, M. A.; Tawata, S. ‘Cytotoxic desulfated saponin from Holothuria atra shows high binding affinity to the oncogenic kinase PAK1: a combined in vitro and in silico study’ Scientia Pharmaceutica, 2018, 86(3), 32. https://doi.org/10.3390/scipharm86030032. Publisher: Multidisciplinary Digital Institute (MPDI), Switzerland.
(26) Junaid, M.; Alam, M. J.; Hossain, M, K.; Halim, M. A.; Ullah, M. O. ‘Molecular Docking and Dynamics of Nickel-Schiff base Complexes for inhibiting Β-lactamase of Mycobacterium Tuberculosis.’ In Silico Pharmacology, 2018, 6, 1-11. DOI: 10.1007/s40203-018-0044-6 Publisher: Springer, Germany
(25) Hoque, M. A.; Rana, S.; Molla, M. R.; Alam, M. M.; Rub, M. A.; Halim, M. A.; Akhtar, F.; Khan, M. A. “Interaction of cetyltrimethylammonium bromide with drug in aqueous/electrolyte solution: A Conductometric and Molecular Dynamics Method Study’’ Chinese Journal of Chemical Engineering, 2018, 26, 159-167 https://doi.org/10.1016/j.cjche.2017.06.016 Publisher: Elsevier, Netherlands
(24) Shawon, J.; Khan, A. M.; Rahman, A.; Hoque, M. M.; khan, M. A. K.; Sarwar, M. S.; Halim, M. A. ‘Molecular Recognition of Azelaic Acid and Related Molecules with DNA polymerase I Investigated by Molecular Modelling Calculations’ Interdisciplinary Sciences: Computational Life Sciences, 2018, 10, 525–537. doi:10.1007/s12539-016-0186-3. Publisher: Springer, Germany
2017
(23) Daly, S.; Knight, G.; Halim, M. A.; Kulesza, A.; MacAleese, L; Antoine, R.; Dugourd, P. “Action-FRET of a Gaseous Protein” Journal of American Society for Mass Spectrometry 2017, 28, 38-49. doi:10.1007/s13361-016-1449-2. Publisher: American Society for Mass Spectrometry, USA
(22) Hoque, M. A.; Alam, M. M.; Rana, S.; Molla, M. R.; Rub, M. A.; Halim, M. A.; Khan, M. A.;“ Effect of Salts and Temperature on the Interaction of Levofloxacin Hemihydrate Drug with Cetyltrimethylammonium Bromide: A Combined Conductometric and Molecular Dynamics Method Study’’ Journal of Molecular Liquid, 2017, 244, 512-520. https://doi.org/10.1016/j.molliq.2017.09.004. Publisher: Elsevier, Netherlands
(21) Rahman, M. S.; Hossain, S. M.; Rahman, M. T.; Halim, M. A.; Ishtiak, M. N.; Kabir, M. Determination of Trace Metal Concentration in Compost, DAP, and TSP Fertilizers by Neutron Activation Analysis (NAA) and Insights from Density Functional Theory Calculations. Environmental Monitoring and Assessment 2017, 189 (12), 618 DOI: 10.1007/s10661-017-6328-1. Publisher: Springer, Germany
(20) Khan, A.; Shawon, J.; Halim, M. A. “Multiple Receptor Conformers based Molecular Docking study of Fluorine Enhanced Ethionamide with Mycobacterium Enoyl ACP Reductase (InhA)” Journal of Molecular Graphics and Modelling, 2017, 77, 386-398, https://doi.org/10.1016/j.jmgm.2017.09.010 Publisher: Elsevier, Netherlands
(19) Zangrando, E., Begum M. S.; Sheikh, M. C.; Miyatake, R.; Hossain, M. M.; Alam, M. M.; Hasnat, M. A.; Halim, M. A.; Ahmed, S.; Rahman, M. N.; Ghosh, A. “Synthesis, characterization, density functional study and antimicrobial evaluation of a series of bischelated complexes with a dithiocarbazate Schiff base ligand. ” Arabian Journal of Chemistry 2017, 10, 172-184. https://doi.org/10.1016/j.arabjc.2016.07.019 Publisher: Elsevier, Netherlands
(18) Naseem, S., Khalid, M., Tahir, M.N., Halim, M.A., Braga, A.A.C., Naseer, M. M., Shafiq, Z. “Synthesis, structural, DFT studies, docking and antibacterial activity of xanthene based hydrazone ligand.” Journal of Molecular Structure. 2017, 1143, 235–244. https://doi.org/10.1016/j.molstruc.2017.04.093. Publisher: Elsevier, Netherlands
(17) Hoque, M. A.; Patoary, M. O. F.; Molla, M. R.; Halim, M. A.; Khan, M. A.; Rub, M. A.‘Interaction Between Cetylpyridinium Chloride and Amino Acids: A Conductomertic and Computational Method Study’ Journal of Dispersion Science and Technology, 2017, 38, 1578–1587. http://dx.doi.org/10.1080/01932691.2016.1262779. Publisher: Taylor & Francis, UK
(16) Adeel, M.; Braga, A. A. C.; Tahir, M. N.; Haq, F.; Khalid, M.; Halim, M. A. “Synthesis, X-Ray Crystallographic, Spectroscopic and Computational Studies of Aminothiazole Derivatives.” Journal of Molecular Structure 2017, 1131, 136–148.https://doi.org/10.1016/j.molstruc.2016.11.046. Publisher: Elsevier, Netherlands
2016
(15) Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization.” Journal of American Society for Mass Spectrometry 2016, 27, 1435-1442. doi:10.1007/s13361-016-1419-8 (Cover Article) Publisher: American Society for Mass Spectrometry, USA
(14) Halim, M. A.; Girod, M.; MacAleese, L.; Lemoine, J.; Antoine, R.; Dugourd, P. “213 nm Ultraviolet Photodissociation on Peptide Anions: Radical-Directed Fragmentation Patterns.” Journal of American Society for Mass Spectrometry 2016, 27, 474-486. DOI: 10.1007/s13361-015-1297-5. Publisher: American Society for Mass Spectrometry, USA
(13) Rahman, A.; Ali, M. T.; Shawan, M. A. K.; Sarwar, M. G.; Khan, M. A. K. Halim, M. A.*; “Halogen-directed Drug Design for Alzheimer’s disease: A Density Functional and Molecular Docking Study. SpringerPlus, 2016, 5, 1345. DOI: 10.1186/s40064-016-2996-5. Publisher: Springer, Germany
(12) Saleh, M. A.; Solayman, M.; Hoque, M. M.; khan, M. A. K.; Sarwar, M. S.; Halim, M. A. “Inhibition of DNA Topoisomerase Type IIα (TOP2A) by Mitoxantrone and Its Halogenated Derivatives: A Combined Density Functional and Molecular Docking Study.” Biomed Research International 2016, Article ID 6817502, 12 pages. http://dx.doi.org/10.1155/2016/6817502. Publisher: Hindawi, Egypt.
(11) Rahman, A.; Hoque, M. M.; khan, M. A. K.; Sarwar, M. S.; Halim, M. A.* “Non-covalent interactions involving halogenated derivatives of capecitabine and thymidylate synthase: a computational approach.” Springer Plus 2016, 5, 146. DOI: 10.1186/s40064-016-1844-y. Publisher: Springer, Germany
(10) Killoran, R. C.; Sowole, M. A.; Halim, M. A.; Konermann, L.; Choy, W.-Y. “Conformational Characterization of the Intrinsically Disordered Protein Chibby: Interplay between Structural Elements in Target Recognition” Protein Science, 2016, 25, 1420-1429. DOI: 10.1002/pro.2936. Publisher: John Wiley & Sons, USA
2010-2015
(9) Enamullah, M.; Quddus, A.; Islam, M. K.; Halim, M. A.;Vasylyeva, V.; Janiak, C. “Switching from 4+1 to 4+2 zinc coordination number through the methyl group position on the pyridyl ligand in the geometric isomers bis[N-2-(4/6-methyl-pyridyl)salicylaldiminato-k2N,O]zinc(II)” Inorganica Chemica Acta 2015, 427, 103-111. https://doi.org/10.1016/j.ica.2014.11.020. Publisher: Elsevier, Netherlands
(8) Hoque, M. M; Halim, M. A.; Sarwar, M. G.; Khan, M. W. “Palladium (ІІ) chloride catalyzed cyclization of 2-alkynyl-4-substituted-N-ethanoyl aniline: Synthesis, Structural and Mechanistic Study” Journal of Physical Organic Chemistry 2015, 28, 732-742. DOI: 10.1002/poc.3477. Publisher: John Wiley & Sons, USA
(7) Hossain, E. M.; Hasan, M. M.; Halim. M. E.; Ehsan, M. Q.; Halim, M. A.* “Interaction between Transition Metals and Phenylalanine: A Combined Experimental and Computational Study”, Spectrochimica Acta Part A: 2015, 138, 499-508. https://doi.org/10.1016/j.saa.2014.11.084. Publisher: Elsevier, Netherlands
(6) Enamuallah, M.; Islam, M. K.; Halim, M. A.; Janiak, C. “Syntheses, spectroscopy, thermal analysis, cyclovoltammetry, X-ray, and TD-DFT analyses on Rh(η4-cod)-enantiopure aminocarboxylate complexes” Journal of Molecular Structure 2015, 1099, 154-162. DOI:10.1016/j.molstruc.2015.06.040. Publisher: Elsevier, Netherlands
(5) Halim, M. A.; Almatarneh, M. H.; Poirier, R. A. “Mechanistic Study of the Deamidation of Glutamine: A Computational Approach” Journal of Physical Chemistry B 2014, 118, 2316-2330. DOI: 10.1021/jp4107266. Publisher: American Chemical Society, USA.
(4) Goni, M. A.; Ahmad, J. U.; Halim, M. A.; Mottalib, M. A.; Chowdhury, D. A. “Uptake and Translocation of Metals in Different Parts of Crop Plants Irrigated with Contaminated Water from DEPZ Area of Bangladesh.” Bulletin of Environmental Contamination Toxicology 2014, 92, 726-732. doi:10.1007/s00128-014-1264-z. Publisher: Springer, Germany
(3) Halim, M.A. ‘Harnessing Sun’s Energy with Quantum Dots Based Next Generation Solar Cell.’ Nanomaterials 2013, 3, 22-47. Publisher: Multidisciplinary Digital Institute (MPDI), Switzerland.
(2) Hoque, M. M.; Halim, M. A.; Rahman, M. M.; Hossain, M. I.; Khan, M. W. “Synthesis and Structural Insights of Substituted 2-iodoacetanilides and 2-iodoanilines”, Journal of Molecular Structure, 2013, 1054-1055, 364-374. https://doi.org/10.1016/j.molstruc.2013.10.011. Publisher: Elsevier, Netherlands
(1) Halim, M. A.; Shaw, D. M.; Poirier, R. A. “Medium Effect on the Equilibrium Geometries, Vibrational Frequencies and Solvation Energies of Sulfanilamide”, Journal of Molecular Structure: THEOCHEM, 2010, 960, 63-72. https://doi.org/10.1016/j.theochem.2010.08.027. Publisher: Elsevier, Netherlands
