Popular GitHub Repositories for Protein

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

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

A collection of research papers for AI-based protein design

Protein-compound affinity prediction through unified RNN-CNN

Neural Networks for Protein Sequence Alignment

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

A Text-guided Protein Design Framework, Nat Mach Intell 2025

Large Language Models in Protein: A Comprehensive Survey

? ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality Protein Backbone Generation

? Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2024).

Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

Must-read papers on NLP for science.

Codebase of paper "Structure Language Models for Protein Conformation Generation" (ICLR'25)

LM-GVP: A Generalizable Deep Learning Framework for Protein Property Prediction from Sequence and Structure

? Augmenting zero-shot mutant prediction by retrieval-based logits fusion.

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction (Briefings in Bioinformatics 2023)

Biological prediction models made simple.

Guided Conditional Wasserstein GAN for De Novo Protein Design

An implementation of ESM2 in Equinox+JAX