In June, Zach McLean, a third year PhD student in Scott Belcher’s lab, was selected and fully funded to attend the NSF-funded CompBio Asia 2025 Workshop. CompBio Asia is a hands-on advanced computational biology workshop designed to teach graduate students how to perform computational workflows and analyze complex datasets. Zach traveled to Bangkok, Thailand, from June 15th to June 28th to attend the workshop at Kasetsart University, this year’s host institution. The event brought together students and instructors from nine different countries.

The workshop focused on five main computational workflows: molecular dynamics, artificial intelligence, protein structure prediction, biomolecule-ligand affinity estimation, and genomic annotation. It began with foundational lectures from field experts and then quickly transitioned into hands-on activities and individual research projects. In addition to the specific workflows, students also learned the basics of UNIX, shell scripting, and how to interact with virtual machines.

Zach’s research project at CompBio Asia involved using molecular dynamics to explore the mechanism of PFAS binding to the major dairy protein, ß-Lactoglobulin. Using the skills gained at the workshop, the student ran molecular dynamics simulations of ß-Lactoglobulin-PFAS interactions using AMBER on a high-performance computing cluster. They utilized tools like Jupyter notebooks to integrate AmberTools packages from Python scripts, which helped parametrize their experimental system for molecular dynamics. The student also employed bash scripts to run AmberTools programs and perform complex calculations, such as molecular mechanics generalized born surface area (MM-GBSA), to analyze the simulation results.

Overall, CompBio Asia 2025 provided an incredible opportunity to learn computational skills in an engaging and effective way. The experience is highly recommended for any other students in the Toxicology Graduate Program interested in computational methods.