zw2x

AI2BMD

AI-powered ab initio biomolecular dynamics simulation

alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

megalodon

Reference implementation of Megalodon 7B model

FLEXS

Fitness landscape exploration sandbox for biological sequence design.

Diffusion-LM

Diffusion-LM

G-SchNet

G-SchNet - a generative model for 3d molecular structures

pensa

PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.

Auto3D_pkg

Auto3D generates low-energy conformers from SMILES/SDF

arpeggio

Calculation of interatomic interactions in molecular structures

AutoDock-Vina

AutoDock Vina

e3_diffusion_for_molecules

BindingSitesFromFragments

De novo design of small molecule binding sites into proteins

x-transformers

A concise but complete full-attention transformer with a set of promising experimental features from various papers

enzyme-datasets

Enzyme datasets used to benchmark enzyme-substrate promiscuity models

AutoDock-GPU

AutoDock for GPUs and other accelerators

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

ColabDesign

Making Protein Design accessible to all via Google Colab!

pytorch_geometric

Graph Neural Network Library for PyTorch

flowtorch

This library would form a permanent home for reusable components for deep probabilistic programming. The library would form and harness a community of users and contributors by focusing initially on complete infra and documentation for how to use and create components.

FLIP

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

awesome-equivariant-network

Paper list for equivariant neural network

FastFold

Optimizing AlphaFold Training and Inference on GPU Clusters

localpdb

Python package to manage protein structures and their annotations

dMaSIF

dlpack

common in-memory tensor structure

moolib

A library for distributed ML training with PyTorch

alphafold

Open source code for AlphaFold.

gemmi

macromolecular crystallography library and utilities

badwolf

A Vim color scheme.