msultan

gpt4all

GPT4All: Run Local LLMs on Any Device. Open-source and available for commercial use.

ColossalAI

Making large AI models cheaper, faster and more accessible

nanoGPT

The simplest, fastest repository for training/finetuning medium-sized GPTs.

tuning_playbook

A playbook for systematically maximizing the performance of deep learning models.

imagen-pytorch

Implementation of Imagen, Google's Text-to-Image Neural Network, in Pytorch

pyprobml

Python code for "Probabilistic Machine learning" book by Kevin Murphy

learning-notes

Notes on books I read, talks I watch, articles I study, and papers I love

RFdiffusion

Code for running RFdiffusion

uncertainty-baselines

High-quality implementations of standard and SOTA methods on a variety of tasks.

papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

chroma

A generative model for programmable protein design

PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

se3_diffusion

Implementation for SE(3) diffusion model with application to protein backbone generation

ProteinFlow

Versatile computational pipeline for processing protein structure data for deep learning applications.

targetdiff

The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)

Meeko

Interfacing RDKit and AutoDock

PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

bio-transformers

bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.

IgLM

Generative Language Modeling for Antibody Design

TRILL

Sandbox for Deep-Learning based Computational Protein Design

biodiffusion

A list of manuscripts/tools using diffusion on biological enttieis

Computational-ADME

peptides.py

Physicochemical properties, indices and descriptors for amino-acid sequences.

TCRdock

python tools for TCR:peptide-MHC modeling and analysis

BO-LIFT

BayesOpt + LIFT

matcher

Matcher is a tool for understanding how chemical structure optimization problems have been solved. Matcher enables deep control over searching structure/activity relationships (SAR) derived from large datasets, and takes the form of an accessible web application with simple deployment. Matcher is built around the mmpdb platform.

SQUID

Official implementation of "Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design"

synspace

Synthesis generative model

insitro-research

Insitro's repository for public research code and data

matcher-mmpdb