Computational structural biology work focused on predicting and analyzing protein-protein interactions using AlphaFold3, followed by structural visualization and interpretation with ChimeraX and PyMOL.
At the UCI proteomics lab, I worked with computational protein structure prediction to investigate binary protein complexes. More than 20 complexes were modeled and evaluated using AlphaFold3, with downstream visualization and structural analysis performed in ChimeraX and PyMOL.
Modeled and evaluated a series of binary protein complexes to examine predicted structures and potential interactions.
Used AlphaFold3 to generate structural predictions for protein-protein complexes.
Examined confidence metrics and visualized predicted structures to assess model quality and interactions.
The project moved from protein sequence preparation through structure prediction, confidence evaluation, visualization, and biological interpretation.
AlphaFold3 predictions were not treated as simply correct or incorrect. I examined model confidence and structural context to understand how reliable each predicted complex was.
Predicted Template Modeling score used as a measure of confidence in the overall predicted protein structure.
Interface predicted Template Modeling score used to assess confidence in the predicted relative arrangement of interacting proteins.
Predicted Aligned Error used to examine uncertainty in relative positions between structural regions and protein partners.
Confidence metrics were considered alongside visual inspection rather than being interpreted in isolation.
Predicted complexes were examined in molecular visualization software to better understand protein interfaces, relative orientation, and overall structural organization.
Used for interactive visualization and inspection of AlphaFold3 predicted protein complexes.
Used to visualize molecular structures and examine predicted protein-protein interfaces.
Connected computational confidence metrics with the physical appearance and organization of predicted complexes.
The project was documented throughout the modeling process, including computational predictions, structural analysis, and research progress.
View the research presentation documenting the computational modeling work and progress from the UCI proteomics project.
Protein function is often determined by interactions with other proteins and molecular components. Modeling complexes provides a way to investigate these relationships at the structural level.
Examining binary complexes provides a structural perspective on how proteins may interact and organize into larger molecular systems.
The project also motivated exploration of larger assemblies involving additional protein partners and nucleic acid components.
A future direction is to move beyond simple binary complexes toward larger molecular assemblies. This includes investigating additional protein partners and nucleic acid components while continuing to evaluate prediction confidence and structural plausibility.
My work focused on the computational modeling and structural interpretation side of the project.