Publications

VIPER: A General Model for Prediction of Enzyme Substrates

CITATIONS: 3 | SOLE AUTHOR | PREPRINT

Here, we introduce VIPER (Virtual Interaction Predictor for Enzyme Reactivity), a model that achieves an average 30% improvement over the previous state-of-the-art model (ProSmith) in reaction prediction for unseen substrates.

RustSASA: A Rust Crate for Accelerated Solvent Accessible Surface Area Calculations

CITATIONS: 0 | SOLE AUTHOR | Journal of Open Source Sofrware

RustSASA overcomes the computational bottlenecks of traditional solvent acesssile surface area (SASA) algorithms, achieving up to a 5× speed increase over FreeSASA. RustSASA integrates seamlessly with Python and the MDAnalysis framework.

Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition

CITATIONS: 14 | MIDDLE AUTHOR | PREPRINT

In this report, we summarize and analyze the 2024 Adaptyv EGFR protein design competition. Participants used computational and ML methods of their choice to design proteins to bind the EGFR, a key drug target that plays a critical role in cell growth, differentiation, and cancer development.