Repositories
timodonnell/papersimreading
Reference management via dropbox
timodonnell/snowball-protein-design
timodonnell/struct2token
Adaptive all-atom tokenization of arbitrary proteins, nucleic acids, and small molecules
timodonnell/llm-benchmark-experiments
Small experiments on benchmarking LLMs
timodonnell/mutinfer
experiments in mutation effect prediction
timodonnell/pyconfind
Python implementation of ConFind from Grigoryan Lab
timodonnell/biocorpus
Explorations in biology-focused pre-training datasets for LLMs
timodonnell/timodonnell.github.io
timodonnell/contactdoc
timodonnell/LlamaFold-experiments
timodonnell/viz-bio2token
Visualize bio2token encodings
timodonnell/TokenFold
Toy project for claude
timodonnell/ProteinEBM-experiments
timodonnell/boltzgen-experiments
timodonnell/huggingface.js
Use Hugging Face with JavaScript
timodonnell/alphafold3
AlphaFold 3 inference pipeline.
timodonnell/boltz
timodonnell/RFdiffusion
Code for running RFdiffusion
timodonnell/proteinpile
Manage protein design experiments
timodonnell/manuscript_ab_epitope_interaction
timodonnell/boltz-metaflow
Docker image and metaflow scripts for running the boltz-1 molecular structure predictor
timodonnell/yabul
Yet Another Bioinformatics Utilities Library
timodonnell/OmegaFold
OmegaFold Release Code
timodonnell/ProteinMPNN
This fork modifies ProteinMPNN to be (mostly) usable as a Python library
timodonnell/RFDesign
This fork modifies RFDesign to be (mostly) usable as a Python library
timodonnell/openfold-dev
Scratch space for experiments with OpenFold
timodonnell/openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
timodonnell/mhcgnomes
Parsing MHC nomenclature in the wild
timodonnell/bamread
Bam to Pandas DataFrame, quickly