Exploring RNA Triple Helices and Protein-Binding Partners using Computational Tools
The Brown laboratory is interested in the structure and function of the MALAT1 RNA triple helix and its protein-binding partners, particularly in the context of cancer and Miller-Dieker Syndrome, which is a rare neurogenetic disease. To that end, the lab uses Python, AlphaFold, PyMOL, FPocketR, and other computational tools to analyze publicly available "omics" data, to examine 3D structure, gene expression, RNA modifications, screen for small molecule binders and generate figures. We have multiple computational projects. Therefore, it is easier to discuss project details in person.
We recently solved a novel 3D structure that will hopefully open new avenues to establish nature's triplexome (i.e. develop tools to identify naturally occurring RNA triple helices, their function, protein-binding partners and implications in health and disease). The Brown laboratory is a relatively small lab, allowing for greater supervision and guidance. After training, undergraduate researchers are expected to master unfamiliar software, navigating that process more independently, because we never know where the science will lead us.