Brian Naughton's starred repositories
RAGatouille
Easily use and train state of the art late-interaction retrieval methods (ColBERT) in any RAG pipeline. Designed for modularity and ease-of-use, backed by research.
ProteinMPNN
Code for the ProteinMPNN paper
rd-blender-docker
A collection of Docker containers for running Blender headless or distributed ✨
www_personal
Personal Webpage
openmm-tutorial-msbs
OpenMM tutorial for the MSBS course
alphafill
AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
gpt_pdf_md
🚀 gpt_pdf_md: Convert PDF to Markdown with GPT-4V & more. Extract images, upload to Google Cloud, & generate Markdown with images. Python, GPT-4V Vision, Scala. Ideal for developers, researchers. PDF to Markdown, GPT-4V, image extraction, Python package
PubMed2PDF
A Python package to download full article PDFs from OA publications
tfold-release
TFold v1.0
Graphinity
Graphinity: Equivariant Graph Neural Network Architecture for Predicting Change in Antibody-Antigen Binding Affinity
8H9-Model-Essentials-Public
Pharmacokinetic Modeling and Optimization of Omburtamab (8H9) Delivered Through the CSF