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a-r-j/README.md

Hi there 👋

  • 🔭 I’m a PhD student at the University of Cambridge. I work on deep learning applied to structural biology and drug discovery.

  • I'm currently doing things with proteins at Genentech / Roche / Prescient Design

  • Previously, I was a visiting researcher at EPFL and MILA, AI Resident at X - The Moonshot Factory (formerly Google X) and an ML Consultant at Relation Therapeutics.

  • 🌱 I’m currently developing Graphein, a data processing library for geometric deep learning in biology.

    • Graphein supports construction and featurisation of:
      • Protein structure graphs
      • Protein meshes
      • Small molecule graphs
      • RNA structure graphs
      • Protein-protein interaction graphs
      • Gene regulatory interaction graphs
  • 📫 How to reach me:

Pinned

  1. graphein graphein Public

    Protein Graph Library

    Jupyter Notebook 975 121

  2. ProteinWorkshop ProteinWorkshop Public

    Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

    Python 140 13

  3. molstar/VSCoding-Sequence molstar/VSCoding-Sequence Public

    VSCode Extension for interactively visualising protein structure data in the editor

    TypeScript 92 8

  4. BioPandas/biopandas BioPandas/biopandas Public

    Working with molecular structures in pandas DataFrames

    Python 679 115

  5. CPDB CPDB Public

    Cython implementation of PDB -> DataFrame parsing

    Cython 16

  6. Ryan-Rhys/The-Photoswitch-Dataset Ryan-Rhys/The-Photoswitch-Dataset Public

    Repository containing a benchmark dataset for machine learning property prediction of photoswitch molecules: https://pubs.rsc.org/en/content/articlehtml/2022/sc/d2sc04306h

    Python 80 12