Biotherapeutic structure
Structure prediction, molecular modelling, docking, post-MD analysis, Docker-enabled workflows, and PyRosetta-assisted affinity evaluation.
Computational drug development · Translational biology
Turning molecular structure into decisions that can move toward patients.
I’m Ahmed Sameh, a bioinformatics scientist at Proteinea working within translational biology and drug development. I own an immunogenicity prediction and benchmarking pipeline and support structure-guided biotherapeutic decisions across structural prediction, Fc biology, post-MD analysis, developability, and translational risk.
Cairo, Egypt · Open to international bioinformatics roles and graduate opportunities
01 Structure 02 Immunogenicity 03 Fc biology 04 Translation MoleculeEvidenceDecision
3+ yearsBiotherapeutics industry
5Publications & chapters
SilveriGEM 2022 medal
7.0IELTS overall
What I bring
Scientific breadth, anchored in a clear specialty.
My strongest professional edge sits at the intersection of structural bioinformatics, antibody science, and translation—not only running tools, but benchmarking evidence and owning workflows. In addition to OMICs analysis.
Immunogenicity & Fc biology
Pipeline ownership and benchmarking for immunogenicity assessment, grounded in antibody engineering, Fc receptor biology, and developability.
Translational intelligence
Cross-functional support spanning preclinical evidence, early toxicology interpretation, patent analysis, and first-in-human development questions.
Complementary research track
RNA-seq, WGCNA, network comparison, and multi-omics questions in neurodegeneration—supported by an MSc in Biotechnology at AUC.
View research profile ↗Industry role · Proteinea
Ownership across computational design and translational development.
This is my primary professional position: a method-focused account of the pipeline ownership, structural work, and translational judgement I bring to biotherapeutic development.
May 2023 — Present
A structure-to-translation role in biotherapeutic development.
I connect computational evidence with candidate risk, developability, and preclinical questions while protecting confidential therapeutic programs.
May 2023 — Present
IndustryBioinformatics Scientist (MTS)
Translational Biology & Drug Development · Proteinea
- Own immunogenicity prediction workflow development, benchmarking, maintenance, and interpretation.
- Perform protein and RNA structure prediction, molecular modelling, docking, molecular dynamics, and post-MD analysis.
- Apply deep knowledge of Fc biology, receptor interactions, and antibody engineering strategies to design and developability questions.
- Co-develop and benchmark PyRosetta-based tooling for evaluating binding-affinity changes.
- Build Docker-enabled computational workflows for repeatable analysis and handoff.
- Support translational biology through early nonclinical and toxicology-study analysis and scientific patent review.
Details are intentionally method-level to protect confidential therapeutic programs.
Portfolio
Selected software and analysis projects.
Four selected projects spanning structural bioinformatics, reproducible omics, network biology, and work in honest active development.
01Production-minded toolRMSD CalculatorA packaged and tested Python CLI for structural comparison, with benchmarking and multi-version continuous integration.Python · Biopython · pytest · CI
02Reproducible workflowSnakeDEGA modular, configuration-driven Snakemake workflow from paired-end RNA-seq reads through differential expression.Snakemake · R · Conda · RNA-seq
03Network biologyCognitive Aging ReanalysisAn independent R Markdown reanalysis using differential expression, enrichment, WGCNA, and network comparison.R · WGCNA · limma · Reporting
04In active developmentBinderFlowA developing Nextflow workflow for generative binder design. RFdiffusion is implemented; sequence design, structure prediction, and ranking remain planned.Nextflow · RFdiffusion · Docker
Explore all repositories on GitHub ↗
Research record
Five peer-reviewed contributions across neurodegeneration, translational evidence, and antimicrobial research.
My academic work spans wet-lab and computational biology. The unifying habit is the same: turn a biological question into evidence that can survive scrutiny.
Google ScholarOMICS and bioinformatics in Parkinson disease and related movement disorders
Academic Press · Book chapter
Modeling Parkinson’s disease with the alpha-synuclein protein
Academic Press · Book chapter
Efficacy and safety of stem cell transplantation for multiple sclerosis
Scientific Reports · Systematic review and meta-analysis
DFT and QSAR study of COMT as inhibitors for Parkinson’s disease treatment
Optical and Quantum Electronics
Bee venom as an alternative for antibiotics against Staphylococcus aureus infections
Scientific Reports · First author
Education & recognition
Building toward network medicine in neurodegeneration.
My developing MSc direction centers on network analysis and WGCNA across disease states in Parkinson’s or Alzheimer’s disease; the exact topic and advisor are not yet finalized.
MSc in Biotechnology
The American University in Cairo
Developing interests in neuroimmunology, multi-omics integration, WGCNA, network biology, and machine learning.
BSc in Biotechnology & Biomolecular Chemistry
Faculty of Science, Cairo University
Graduated Excellent with Honors. The graduation project ranked first and became a first-author publication.
Diploma in Machine Learning for Bioinformatics
Eg-CompBio, Egypt
Supervised learning, unsupervised learning, and reinforcement learning.
Adaptyv Bio protein-design competition
Dry-lab leader, CU_Egypt iGEM team
Published first-author in Scientific Reports
German Goethe-Zertifikat B1
Let’s connect
Looking for a scientist who can connect structure, biology, and translation?
I’m open to international bioinformatics roles, research collaborations, and MSc/PhD opportunities aligned with structural or systems bioinformatics.