Some Projects ⁴

Some research projects I’m interested in and actively working on include

1. My main DPhil research is focused on generative modelling of protein folding trajectories. Given a 3D structure, can we train models using frameworks like Diffusion and Flow Matching to generatively predict possible folding pathways in a trajectory fashion that map to empirical data such as phi-value analysis and MD simulations of protein folding. Particularly interesting is whether any sufficiently performing model is learning implicit physics (or enforcing such physics in the training regime) that can appropriately capture natural folding energy landscapes and be exploitable for perturbation analysis and drug target identification.

2. Inspired by a recent paper AbMelt I’ve spent some months putting together a python package for the simulation of antibody Fv regions with GROMACS at high temperature (350K) for ML prediction of their thermostability (Tm) from MD features: HOGROAST

Initial results from this work suggest that the training set of antibodies is likely a major determinant of the effectiveness of the learned prediction models as my initial results were significantly worse at prediction on the test set than AbMelt’s. We came to this conclusion because our training set was taken from Jain et al. consisting of a very diverse set of IgGs whilst, although their training data is unavailable for us to confirm this, I expect that AbMelt trained on a more closely related set of mAbs from a potentially clinical pipeline.

Fun side projects I try fit into my spare time include home server labbing (DIY micro-HPC building) with Raspberry Pis and old computers I’ve gathered over the years, and modding vintage games such as Mount & Blade Warband. Alongside this website of course!