Stars
A fully open source biomolecular structure prediction model based on AlphaFold3
"AI-Trader: Can AI Beat the Market?" Live Trading Bench: https://ai4trade.ai
Sidechain conditioning and modeling for full-atom protein sequence design
BindCraft modified to make PyRosetta use and installation optional: no license needed
Potts model-based protein sequence design
A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS
Official repository for the ProteinDJ protein design pipeline
Codebase for Germinal, a broadly enabling generative pipeline for efficient generation of epitope-targeted de novo antibodies.
Application to assign secondary structure to proteins
SpatialPPIv2: Enhancing protein–protein interaction prediction through graph neural networks with protein language models.
Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3
List of papers about Proteins Design using Deep Learning
Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning
Foldseek enables fast and sensitive comparisons of large structure sets.
A Unified Evaluation Suite for Protein Design
Multi-class signal peptide prediction and structure decoding model.
Improved antibody structure-based design using inverse folding
DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models
Graph transformer for estimating protein model accuracy
Extension of ThermoMPNN for double mutant predictions
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361
Official Repository for the Uni-Mol Series Methods