Projects in computational chemistry

Protein Dynamics and Binding Site Discovery
I developed and implemented workflows that incorporate ligand stability molecular dynamics simulations, docking, and other physics-based methods to analyze protein dynamics and identify potential therapeutic binding sites. We then used this workflow to identify a novel binding pocket in a protein target without a prior co-crystal structure, later confirmed by in-house crystallography. In one of the projects, I manage collaboration with D.E. Shaw Research, where I leveraged their long-timescale molecular dynamics simulations to illustrate protein dynamics relevant to disease state.

Medium-to-Large Molecule Design and Optimization
I led the creation of first in-house workflow for designing peptidic large molecules, combining AI-based protein structure prediction tools (AlphaFold2, RoseTTAFoldAllAtom) with molecular dynamics simulations. This resulted in a validated hit, confirmed through biophysical assays. In parallel, I spearheaded a project to enhance nanobody affinity and expression levels using similar computational techniques. These optimized nanobodies have been experimentally validated and are now essential in advancing our structure-based drug discovery efforts. Lastly, I developed a first in-house protocol for generating macrocycle conformations and their physical properties combining QM and MM-based methods. The workflow is meant to assist medicinal chemists in their decisions around which macrocycles to synthesize over others.

Next-Generation Sequencing (NGS) Platform
I also developed the first in-house platform for ingesting and analyzing NGS data across multiple campaigns. This platform enables our teams to make data-driven decisions on experimental directions and compound synthesis.

What I enjoy most about my role is the cross-functional collaboration. Every day, I work alongside medicinal chemists, structural biologists, and biophysicists to align computational strategies with experimental goals, test hypotheses, and brainstorm new experiments. In parallel, I partner with computational infrastructure teams to ensure seamless integration of platforms and workflows.