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KAUST Computational Advances in Structural Biology
Last month, I had the privilege of being invited to the KAUST Research Conference on Computational Advances in Structural Biology, held from May 1-3, 2023. This gave me the opportunity to present some...
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Le Tour de Farce 2023
16:30 BST 27/06/2023 Oxford, UK. A large number of scientists were spotting riding bicycles across town, to the consternation of onlookers. The event was the Oxford Protein Informatics Group (OPIG)...
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The workings of Fragmenstein’s RDKit neighbour-aware minimisation
Fragmenstein is a Python module that combine hits or position a derivative following given templates by being very strict in obeying them. This is done by creating a “monster”, a compound that has the...
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Working with PDB Structures in Pandas
Pandas is one of my favourite data analysis tools working in Python! The data frames offer a lot of power and organization to any data analysis task. Here at OPIG we work with a lot of protein...
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Tracking the change in ML performance for popular small molecule benchmarks
The power of machine learning (ML) techniques has captivated the field of small molecule drug discovery. Increasingly, researchers and organisations have employed ML to create more accurate algorithms...
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The XChem trove of protein–small-molecules structures not in the PDB
The XChem facility at Diamond Light Source is truly impressive feat of automation in fragment-based drug discovery, where visitors comes clutching a styrofoam ice box teeming with apo-form protein...
View ArticleTesting python (or any!) command line applications
Through our work in OPIG, many of our projects come in the form of code bases written in Python. These can be many different things like databases, machine learning models, and other software tools....
View ArticleGenerating Haikus with Llama 3.2
At the recent OPIG retreat, I was tasked with writing the pub quiz. The quiz included five rounds, and it’s always fun to do a couple “how well do you know your group?” style rounds. Since I work with...
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De novo protein padlocks
Binding a desired protein tightly is important for biotechnology. Recent advances in deep learning have allowed the de novo design of (mostly α-helical) binding protein, sidestepping the laborious...
View ArticleThe Sprawl: Slogs in Scribing and Software
“Dead shopping malls rise like mountains beyond mountains. And there’s no end in sight.” Régine Chassagne Sometimes I wonder would my PhD have been simpler if I had broken up the findings into three...
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