Fatima Pardo Avila, PhD

Postdoc

Michael Levitt, Stanford University

Pronouns: she/her

I am a computational structural biologist that has specialized in using computational tools to visualize RNA polymerase and the ribosome in motion. During my postdoc at Michael Levitt’s Lab, I have focused on studying the ribosome. This complex and large system contains approximately 2 million atoms (in a solvated box) making it a challenging system to simulate. However, I have successfully generated molecular dynamics simulations of the ribosome. And in collaboration with Prof. Gunnar von Heijne at Stockholm University, I have been investigating how interactions between the exit tunnel of the ribosome and the nascent protein can regulate translation. My technical expertise has also led to collaborations with Prof. David Baker at the University of Washington, in which I have used molecular dynamics and molecular modeling to assess the designs of cyclic peptides and interleukin mimics.
In 2020, I joined the Stanford Data Science Scholars Program, which deepened my commitment to do and promote open science. This commitment inspired me to take over the PDBCleanV2 project, a tool that allows users to create self-consistent structure datasets. Over the past year, I have worked on building this tool, focusing in improving documentation and making it user-friendly. I hope that this tool will benefit scientists by making it easier to compare available structures.
My postdoc experience has been especially interesting, as it has been intertwined with my recovery from being hit by a car while riding my bike on the Stanford campus at the beginning of my postdoc. During this time, I have learned to manage the challenges from my recovery, while still doing science, mentoring, teaching, and doing outreach, and JEDI work. These difficulties, instead of discouraging me, have only strengthened my commitment to continue doing research and keep working to become a principal investigator.