Popular GitHub Repositories for Protein Docking

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

List of papers about Proteins Design using Deep Learning

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

Implementation of the model from "ProGen: Language Modeling for Protein Generation"

Generation of protein sequences and evolutionary alignments via discrete diffusion models

Diffusion models of protein structure; trigonometry and attention are all you need!

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Scientific Large Language Models: A Survey on Biological & Chemical Domains

GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)

[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models

Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding

A collection of research papers for AI-based protein design

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning

Official Implemetation of DPLM (ICML'24) - Diffusion Language Models Are Versatile Protein Learners

PocketGen (Nature Machine Intelligence 24): Generating Full-Atom Ligand-Binding Protein Pockets

LucaProt: A novel deep learning framework that incorporates protein amino acid sequence and structural information to predict protein function.

Inference code for PoET: A generative model of protein families as sequences-of-sequences