hgbrian

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

mace

MACE - Fast and accurate machine learning interatomic potentials with higher order equivariant message passing.

rd-blender-docker

A collection of Docker containers for running Blender headless or distributed ✨

ProDy

A Python Package for Protein Dynamics Analysis

mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

IgFold

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

tokengt

[NeurIPS'22] Tokenized Graph Transformer (TokenGT), in PyTorch

pypdb

A Python API for the RCSB Protein Data Bank (PDB)

www_personal

Personal Webpage

sage

Proteomics search & quantification so fast that it feels like magic

mhcflurry

Peptide-MHC I binding affinity prediction

Umol

Protein-ligand structure prediction

ANARCI

Antibody Numbering and Antigen Receptor ClassIfication

openmm-tutorial-msbs

OpenMM tutorial for the MSBS course

hotmetal

A tiny HTML generator 🔥🤘

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.

NoLabs

Open source biolab

PyRMD

AI-powered Virtual Screening

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

alphafold2rave

Sapiens

Sapiens is a human antibody language model based on BERT.

tenforty

Python library to compute US federal taxes, and state taxes for some states.

HASTEN

Machine Learning Boosted Docking (HASTEN): Accelerate Structure-based Virtual Screening

PubMed2PDF

A Python package to download full article PDFs from OA publications

protkit

A Unified Approach to Protein Engineering

openmm_deepmd_plugin

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