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★★★★★

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USD 70 /hr

★★★★★

☆☆☆☆☆

Hire Dr. Ahmed S.

Australia

USD 70 /hr

PhD structural immunologist | Protein crystallography, molecular docking & ML for ligand discovery

Profile Summary

Final-year PhD candidate in structural immunology (Monash University, Rossjohn laboratory) with combined wet-lab and computational expertise across protein structure, ligand discovery, and machine learning. I work at the interface of experiment and computation, which means I can both generate structural data and interpret it in ways that translate into real design decisions. Experimental: protein expression and purification, X-ray crystallography from crystallisation optimisation through to refinement, fluorescence polarisation binding assays, and cell-based immunoassays. Computational: molecular docking including covalent and Schiff-base chemistry, protein structure prediction with AlphaFold2-Multimer and Boltz-2, PyRosetta energetics and interface analysis, and machine learning tailored to small experimental datasets (transfer learning, molecular foundation models, Gaussian processes, and active-learning design of experiments). Domain: MHC and MHC-like antigen presentation, protein-ligand binding, and T-cell immunology, with a first-author manuscript in preparation for a high-impact journal. I can help with: virtual screening and docking campaigns with ranked hits and binding-mode analysis; structure prediction and model interpretation; protein-ligand interaction and binding-affinity analysis; ML models for small or noisy datasets; and scientific writing, figure design, and manuscript editing to publication standard. I take on clearly scoped projects with defined deliverables and can work under NDA.

Subject Matter Expertise

• ☆ Computational Biology
• ☆ Basic Immunology
• ☆ Adjuvant & Antigen Research
• ☆ Data Analysis
• ☆ Computer Simulation/Computational Modeling
• ☆ Drug Discovery
• ☆ Structure-Activity Relationship (SAR) Studies

Services

• Writing
• Research
• Consulting

Writing Medical Writing, Non-Medical Regulatory Writing, Audio Transcription, Translation

Research Scientific and Technical Research

Consulting Scientific and Technical Consulting

Work Experience

Teaching Associate

Monash University

February 2025 - Present

PhD candidate

Monash University

February 2024 - Present

Assistant lecturer

Cairo University

November 2017 - Present

Education

MSc

Cairo University

April 2019 - April 2023

BSc

Cairo University

September 2012 - June 2016

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Ahmed Samir, Abdo A. Elfiky, Ibrahim M. Ibrahim, Ahmed M. Elghareib, Yousef S. Bashandy, Mayar M. Hamdy, Rana T. Kamal, Fatma G. Amin, Yomna Elkaramany, Anan M. Rashad, et al. (2023). Simulation of gold nanoparticle movement through normal and cancer cell membranes . Computers in Biology and Medicine.

Ahmed Samir, Jameel M. Abduljalil, Ahmed M. Elghareib, Ahmed A. Ezat, Abdo A. Elfiky(2023). How helpful were molecular dynamics simulations in shaping our understanding of SARS-CoV-2 spike protein dynamics? . International Journal of Biological Macromolecules. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 125153. Elsevier {BV}

Ahmed Samir, Ahmed A. Ezat, Jameel M. Abduljalil, Ahmed M. Elghareib, Abdo A. Elfiky(2023). The discovery of novel antivirals for the treatment of mpox: is drug repurposing the answer? . Expert Opinion on Drug Discovery. 18. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 551--561. Informa {UK} Limited

Ahmed Samir, Mohamed M. Fathy, Abdo A. Elfiky, Yousef S. Bashandy, Mayar M. Hamdy, Ahmed M. Elgharib, Ibrahim M. Ibrahim, Rana T. Kamal, Ahmed S. Mohamed, Anan M. Rashad, et al.(2023). An insight into synthesis and antitumor activity of citrate and gallate stabilizing gold nanospheres . Scientific Reports. 13. (1). Springer Science and Business Media {LLC}

Ahmed Samir, Wael Elshemey, Abdo Elfiky(2022). Can de-phosphorylation of serine-5 in the C-terminal domain of human polymerase II affect its interaction with the PA C-terminal domain of bat Flu A polymerase? . Journal of Biomolecular Structure and Dynamics. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--10. Informa {UK} Limited