About Me
Computational biology PhD student working on protein structure, nanobody therapeutics, and large-scale MD simulations.
Fareeda Abu-Juam
PhD Student • Computational Structural Biology • CMU–Pitt Joint Program
I study protein–protein interactions using large-scale molecular dynamics (MD) and structure-aware machine learning to understand therapeutic escape and guide protein design.
Links:
- GitHub
- Google Scholar
- Email: fea54 [at] pitt [dot] edu
Research Focus
- Nanobody Design and Simulation
- Structure-informed ML for therapeutic engineering
Featured Work
🧬 Omicron–Nanobody Binding Dynamics
Goal: Identify mutation-induced interface changes that disrupt binding.
Methods: All-atom MD, interface contact statistics, covariance interaction scoring.
Output: Mechanistic insight + candidate engineering targets.
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🤖 AlphaFold Screening & Convergence
Goal: Understand when/why models converge to confident complexes.
Methods: ipTM/pTM/PAE trends across recycles, early-stop heuristics, benchmarking.
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🔬 Covariance-Based Interaction Scoring
Goal: Rapidly summarize stabilizing vs destabilizing interactions from MD.
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