Researchers from Apple have released SimpleFold, a protein structure prediction model which uses exclusively standard Transformer layers. The results seem to show that SimpleFold is a little less accurate than methods such as AlphaFold2, but much faster and easier to integrate into standard LLM-like workflows. SimpleFold also shows very good scaling performance, in line with other Transformer models like ESM2. So what is powering this seemingly simple development?
Continue readingRecently, I have been conducting a project in which I need to predict the structures of a dataset comprising a few thousand protein sequences using AlphaFold 3. Taking a naive approach, it was taking an hour or two per entry to get a predicted structure. With a few thousand structures, it seemed that it would take months to be able to run…
In this blog post, I will go through some tips I found to help accelerate the structure predictions and make all of the predictions I needed in under a week. In general, following the tips in the AlphaFold 3 performance documentation is a useful starting place. Most of the tips I provide are related to accelerating the MSA generation portion of the predictions because this was the biggest bottleneck in my case.
Continue readingThe pharmaceutical industry is undergoing a profound transformation, driven by the promise of Artificial Intelligence (AI) and Machine Learning (ML). These technologies offer the potential to escape the industry’s persistent challenges of high costs, protracted development timelines, and staggering failure rates. From accelerating the identification of novel biological targets to optimizing the properties of lead compounds, AI is poised to enhance the precision and efficiency of drug discovery at nearly every stage
Yet, this revolutionary potential is constrained by a fundamental dependency. The power of modern AI, particularly the deep learning (DL) models that excel at complex pattern recognition, is directly proportional to the volume, diversity, and quality of the data they are trained on. This creates a critical bottleneck: the high-quality experimental data required to train these models—specifically, the protein-ligand binding affinity values that quantify the strength of an interaction—are notoriously scarce, expensive to generate, and often of inconsistent quality or locked within proprietary databases.
Continue readingAll chemistry LLM enthusiasts were treated to a pleasant surprise on Friday when Greg Brockman tweeted that ChatGPT now has access to RDKit. I’ve spent a few hours playing with the updated models and I have summarized some of my findings in this blog.
I recently attended the Learning Meaningful Representations of Life (LMRL) workshop at ICLR 2025. The goal of LMRL is to highlight machine learning methods which extract meaningful or useful properties from unstructured biological data, with an eye towards building a virtual cell. I presented my paper which demonstrates how standard Transformers can learn to meaningfully represent 3D coordinates when trained on protein structures. Each paper submitted to LMRL had to include a “meaningfulness statement” – a short description of how the work presents a meaningful representation.
Continue readingMolecular docking with graph neural networks works by representing the molecules as featurized graphs. In DiffDock, each ligand becomes a graph of atoms (nodes) and bonds (edges), with features assigned to every atom using chemical properties such as atom type, implicit valence and formal charge.
We recently discovered that a change in RDKit versions significantly reduces performance on the PoseBusters benchmark, due to changes in the “implicit valence” feauture. This post walks through:
TL:DR: Use the dependencies listed in the environment.yml file, especially in the case of DiffDock, or your performance could half!
Continue readingAccording to GitHub’s Open Source Survey, Python has officially become the world’s most popular programming language in 2024 – ultimately surpassing JavaScript. Due to its exceptional popularity, NVIDIA announced Python support for its CUDA toolkit at last year’s GTC conference, marking a major leap in the accessibility of GPU computing. With the latest update (https://nvidia.github.io/cuda-python/latest/) and for the first time, developers can write Python code that runs directly on NVIDIA GPUs without the need for intermediate C or C++ code.
Historically tied to C and C++, CUDA has found its way into Python code through third-party wrappers and libraries. Now, the arrival of native support means a smoother, more intuitive experience.
This paradigm shift opens the door for millions of Python programmers – including our scientific community – to build powerful AI and scientific tools without having to switch languages or learn legacy syntax.
Continue readingRecently, I have been interested in adding a confidence metric to the predictions made by a machine learning model I have been working on. In this blog post, I will outline a few strategies I have been exploring to do this. Powerful deep learning models like AlphaFold are great, not only for the predictions they make, but they also generate confidence measures to give the user a sense of how much to trust the prediction.
Continue readingFollowing on from my previous blopig post, Garrett gave the very helpful suggestion of combining Multiple Comparisons Similarity (MCSim) plots to reduce information redundancy. For example, this an MCSim plot from my previous blog post:
This plot shows effect sizes from a statistical test (specifically Tukey HSD) between mean absolute error (MAE) scores for different molecular featurization methods on a benchmark dataset. Red shows that the method on the y-axis has a greater average MAE score than the method on the x-axis; blue shows the inverse. There is redundancy in this plot, as the same information is displayed in both the upper and lower triangles. Instead, we could plot both the effect size and the p-values from a test on the same MCSim.
I’m delighted to report our collaboration (Ísak Valsson, Matthew Warren, Aniket Magarkar, Phil Biggin, & Charlotte Deane), on “Narrowing the gap between machine learning scoring functions and free energy perturbation using augmented data”, has been published in Nature’s Communications Chemistry (https://doi.org/10.1038/s42004-025-01428-y).
During his MSc dissertation project in the Department of Statistics, University of Oxford, OPIG member Ísak Valsson developed an attention-based GNN to predict protein-ligand binding affinity called “AEV-PLIG”. It featurizes a ligand’s atoms using Atomic Environment Vectors to describe the Protein-Ligand Interactions found in a 3D protein-ligand complex. AEV-PLIG is free and open source (BSD 3-Clause), available from GitHub at https://github.com/oxpig/AEV-PLIG, and forked at https://github.com/bigginlab/AEV-PLIG.