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Hire Dr. Marawan A.

Canada

USD 100 /hr

Drug Discovery Consultant; Computational Chemist PhD; Computational Drug Discovery Scientist; Data Scientist

Profile Summary

*Extensive training and experience (10+ years, Ph.D. & Postdoc/RA.) in all aspects of computational chemistry methods relevant to the drug discovery and chemoinformatics fields, that include, but are not limited to: quantum chemical calculations, computational spectroscopy, structure-based drug design including docking, homology modeling, molecular dynamics simulation, free energy calculation; ligand-based drug design including pharmacophore modeling, QSAR, 3D-QSAR, combinatorial library design, target focused library construction, ADME analysis. *Hand-on experience with the state-of-the-art technology stack for data science, such as machine learning tools and packages, Anaconda, Python (> 6years) and its toolkits (e.g. pandas, matplotlib, seaborn/plotly, scikit learn, numpy), Jupyter notebook, Keras, TensorFlow, Linux Bash, R & SQL. In terms of hardware, I have extensive working knowledge with NVIDIA GPU; and I am familiar with Linux, Mac, and Windows OS. *Advanced knowledge with modern drug screening techniques, including fragment screening & linking, pharmacophore- or shape-based database searching, virtual screening (docking & scoring). *Up to date in-depth knowledge with modern software for structure/ligand-based drug design such as Schrodinger, MOE, RDKit, AMBER, NAMD, VMD, and others. *Hand on experience with modern machine/deep learning applications in the fields of drug discovery and their applications using the current state of the art tools that include Tensor-flow, Keras, Deepchem Scikit-learn, H2O, and others. *I have closely worked with synthetic medicinal chemists, pharmacologists, immunologists, biochemists, and physicians. I had the chance to apply the knowledge and skills gained during the PhD to a number of challenging projects in the field of computational drug discovery. I was able to generate the most complete homology model for the human Nav1.5 membrane-embedded ion channel. •I have participated in several projects to find and/or optimize novel, small molecule lead structures against challenging protein targets. Many of these novel small molecules were further validated using experimental biochemical and/or biophysical assays. *Link to my google scholar page: https://scholar.google.ca/citations?user=dMVj160AAAAJ&hl=en *Link to my LinkedIN profile: https://www.linkedin.com/in/marawan-ahmed-24b81155/

Subject Matter Expertise

• ★ Computational Chemistry
• ☆ Molecular Modeling
• ☆ Molecular Docking
• ☆ Chemoinformatics
• ☆ Data Analysis
• ☆ Machine Learning
• ☆ Drug Development

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Copywriting, Newswriting

Research Market Research

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Data Visualization, Big Data Analytics, Data Insights

Work Experience

Data Scientist

Alberta Health Services

November 2018 - Present

Postdoctoral reserach fellow

University of Alberta

July 2014 - November 2018

Education

PhD Theoretical and Computational Chemistry

Swinburne University of Technology, Australia

March 2010 - May 2014

BSc (Hons)

Faculty of Pharmacy, Cairo University

September 2001 - July 2006

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Barakat, Khaled and Ahmed, Marawan and Tabana, Yasser and Ha, Minwoo(2021). A ‘deep dive’into the SARS-Cov-2 polymerase assembly: identifying novel allosteric sites and analyzing the hydrogen bond networks and correlated dynamics. Journal of Biomolecular Structure and Dynamics. p. 1--21. Taylor \& Francis

Ahmed, Marawan and Hasani, Horia Jalily and Kalyaanamoorthy, Subha and Barakat, Khaled(2021). GPCR_LigandClassify.py; a rigorous machine learning classifier for GPCR targeting compounds. Scientific Reports.

Ganesan, Aravindhan and Ahmed, Marawan and Okoye, Isobel and Arutyunova, Elena and Babu, Dinesh and Turnbull, William L and Kundu, Joydeb Kumar and Shields, Justin and Agopsowicz, Katharine Cheryl and Xu, Lai and others(2019). Comprehensive in vitro characterization of PD-L1 small molecule inhibitors. Scientific reports. 9. (1). p. 1--19. Nature Publishing Group

Elsayed, Nevine MY and Serya, Rabah AT and Tolba, Mai F and Ahmed, Marawan and Barakat, Khaled and Abou El Ella, Dalal A and Abouzid, Khaled AM(2019). Design, synthesis, biological evaluation and dynamics simulation of indazole derivatives with antiangiogenic and antiproliferative anticancer activity. Bioorganic chemistry. 82. p. 340--359. Academic Press

Ahmed, Marawan and Kumar, Anil and Hobman, Tom C and Barakat, Khaled(2019). Structure-based screening and validation of potential dengue virus inhibitors through classical and QM/MM affinity estimation. Journal of Molecular Graphics and Modelling. 90. p. 128--143. Elsevier

Jaballah, Maiy Y and Serya, Rabah AT and Saad, Nasser and Khojah, Sohair M and Ahmed, Marawan and Barakat, Khaled and Abouzid, Khaled AM(2019). Towards discovery of novel scaffold with potent antiangiogenic activity; design, synthesis of pyridazine based compounds, impact of hinge interaction, and accessibility of their bioactive conformation on VEGFR-2 activities. Journal of Enzyme Inhibition and Medicinal Chemistry. 34. (1). p. 1573--1589. Taylor \& Francis

Jalily Hasani, Horia and Ganesan, Aravindhan and Ahmed, Marawan and Barakat, Khaled H(2018). Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel. PloS one. 13. (2). p. e0191905. Public Library of Science San Francisco, CA USA

Marawan Ahmed, Khaled Barakat(2017). The Too Many Faces of PD-L1: A Comprehensive Conformational Analysis Study . Biochemistry. 56. (40). p. 5428--5439. American Chemical Society ({ACS})

Ahmed, Marawan and Hasani, Horia Jalily and Ganesan, Aravindhan and Houghton, Michael and Barakat, Khaled(2017). Modeling the human Nav1. 5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade. Drug Design, Development and Therapy. 11. p. 2301. Dove Press

Hasani, Horia Jalily and Ahmed, Marawan and Barakat, Khaled(2017). A comprehensive structural model for the human KCNQ1/KCNE1 ion channel. Journal of Molecular Graphics and Modelling. 78. p. 26--47. Elsevier

Ahmed, Marawan and Barakat, Khaled(2017). The Too Many Faces of PD-L1: A Comprehensive Conformational Analysis Study. Biochemistry. 56. (40). p. 5428--5439. American Chemical Society

Ahmed, Marawan and Barakat, Khaled(2017). When theory meets experiment: the PD-1 challenge. Journal of molecular modeling. 23. (11). p. 1--5. Springer Berlin Heidelberg

Ahmed, Marawan and Pal, Abhishek and Houghton, Michael and Barakat, Khaled(2016). A Comprehensive Computational Analysis for the Binding Modes of Hepatitis C Virus NS5A Inhibitors: The Question of Symmetry. ACS Infectious Diseases. 2. (11). p. 872--881. American Chemical Society

Chatterjee, Subhojyoti and Ahmed, Marawan and Wang, Feng(2016). How similar is the electronic structures of $β$-lactam and alanine?. Radiation Physics and Chemistry. 119. p. 1--8. Pergamon

Ahmed, Marawan and Barakat, Khaled(2015). Baby steps toward modelling the full human programmed Death-1 (PD-1) pathway. Receptors & Clinical Investigation. 2.

El-labbad, Eman M and Ismail, Mohammed AH and Abou Ei Ella, Dalal A and Ahmed, Marawan and Wang, Feng and Barakat, Khaled H and Abouzid, Khaled AM(2015). Discovery of Novel Peptidomimetics as Irreversible CHIKV NsP2 Protease Inhibitors Using Quantum Mechanical-Based Ligand Descriptors. Chemical biology & drug design. 86. (6). p. 1518--1527.

Kassem, Summer and Ahmed, Marawan and El-Sheikh, Salah and Barakat, Khaled H(2015). Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods. Journal of Molecular Graphics and Modelling. 62. p. 105--117. Elsevier

Viricel, Clement and Ahmed, Marawan and Barakat, Khaled(2015). Human PD-1 binds differently to its human ligands: A comprehensive modeling study. Journal of Molecular Graphics and Modelling. 57. p. 131--142. Elsevier

Wang, Feng and Ahmed, Marawan(2015). Sitting above the maze: recent model discoveries in molecular science. Molecular Simulation. 41. (1-3). p. 205--229. Taylor \& Francis

Ahmed, Marawan and Wang, Feng and Levin, Aviad and Le, Connie and Eltayebi, Yomna and Houghton, Michael and Tyrrell, Lorne and Barakat, Khaled(2015). Targeting the Achilles heel of the hepatitis B virus: a review of current treatments against covalently closed circular DNA. Drug discovery today. 20. (5). p. 548--561. Elsevier Current Trends

Feketeova, Linda and Plekan, Oksana and Goonewardane, Mayanthi and Ahmed, Marawan and Albright, Abigail L and White, Jonathan and O’Hair, Richard AJ and Horsman, Michael R and Wang, Feng and Prince, Kevin C(2015). Photoelectron spectra and electronic structures of the radiosensitizer nimorazole and related compounds. The Journal of Physical Chemistry A. 119. (39). p. 9986--9995. American Chemical Society

Sadek, Maiada M and Serrya, Rabah A and Kafafy, Abdel-Hamid N and Ahmed, Marawan and Wang, Feng and Abouzid, Khaled AM(2014). Discovery of new HER2/EGFR dual kinase inhibitors based on the anilinoquinazoline scaffold as potential anti-cancer agents. Journal of enzyme inhibition and medicinal chemistry. 29. (2). p. 215--222. Taylor \& Francis

Ahmed, Marawan and Wang, Feng and Acres, Robert G and Prince, Kevin C(2014). Structures of Cycloserine and 2-Oxazolidinone Probed by X-ray Photoelectron Spectroscopy: Theory and Experiment. The Journal of Physical Chemistry A. 118. (20). p. 3645--3654. ACS Publications

Ahmed, Marawan and Arachchilage, Anoja P Wickrama and Wang, Feng(2013). A QM/MM molecular dynamic simulation and vibrational spectroscopic study of 6-azaCytidine and cytidine. arXiv preprint arXiv:1305.6664.

Iakhnenko, Marianna and Feyer, Vitaliy and Tsud, Nataliya and Plekan, Oksana and Wang, Feng and Ahmed, Marawan and Slobodyanyuk, Oleksandr V and Acres, Robert G and Matol{\'\i}n, Vladim{\'\i}r and Prince, Kevin C(2013). Adsorption of cytosine and aza derivatives of cytidine on Au single crystal surfaces. The Journal of Physical Chemistry C. 117. (36). p. 18423--18433. ACS Publications

Ahmed, Marawan and Yu, Aimin and Wang, Feng(2013). DFT Study on the Conformational and Vibrational Properties of 3'-Deoxycytidine and Its Analogues. International Journal of Chemistry. 5. (2). p. 68. Canadian Center of Science and Education

Ahmed, Marawan and Sadek, Maiada M and Serrya, Rabah A and Kafafy, Abdel-Hamid N and Abouzid, Khaled A and Wang, Feng(2013). Assessment of new anti-HER2 ligands using combined docking, QM/MM scoring and MD simulation. Journal of Molecular Graphics and Modelling. 40. p. 91--98. Elsevier

Ahmed, Marawan and Sadek, Maiada M and Abouzid, Khaled A and Wang, Feng(2013). In silico design: extended molecular dynamic simulations of a new series of dually acting inhibitors against EGFR and HER2. Journal of Molecular Graphics and Modelling. 44. p. 220--231. Elsevier

Ahmed, Marawan and Bird, Stefanie and Wang, Feng and Palombo, Enzo A(2013). In silico investigation of lactone and thiolactone inhibitors in bacterial quorum sensing using molecular modeling. arXiv preprint arXiv:1305.3691.

Ahmed, Marawan and Wang, Feng(2013). Vibrational spectroscopy and intramolecular hydrogen bond network of (didehydro) deoxycytidine nucleosides. Current Physical Chemistry. 3. (2). p. 166--178. Bentham Science Publishers

Ahmed, Marawan and Ganesan, Aravindhan and Wang, Feng and Feyer, Vitaliy and Plekan, Oksana and Prince, Kevin C(2012). Photoelectron spectra of some antibiotic building blocks: 2-azetidinone and thiazolidine-carboxylic acid. The Journal of Physical Chemistry A. 116. (33). p. 8653--8660. ACS Publications

OTHER

Barakat, Khaled and Ahmed, Marawan and Ganesan, Aravindhan and Houghton, Michael and Tyrrell, Lorne(2018). SYSTEMS AND METHODS OF SELECTING COMPOUNDS WITH REDUCED RISK OF CARDIOTOXICITY USING CARDIAC SODIUM ION CHANNEL MODELS.

DISSERTATION THESIS

Ahmed, MarawanQuantum Mechanical Applications in Spectroscopy and Computational Drug Design.