Deep neural models for core NLP tasks (Pytorch version)
An implementation of the DeepMind's AlphaFold based on PyTorch for research
A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
Protein Secondary Structure predictor using Convolutional Neural Networks
Repository containing pipelines developed for the SNAC-DB (Structural NANOBODY® VHH and Antibody Complex Database). SNAC-DB is ML-ready curation of the Protein Data Bank (PDB) for NANOBODY® VHH and antibody complex structures.
Python bindings for the `buildcell` program for Ab Initio Random Structure Searching (AIRSS)
[ACL 2023] SPEECH: Structured Prediction with Energy-Based Event-Centric Hyperspheres
Small, fast, fully differentiable antibody Fv structure predictor in JAX. ~0.76M parameters, matches IgFold on CDR-H3, folds an Fv in ~0.8s on CPU.
Active Imitation Learing with Noisy Guidance
Your open-source alternative to AlphaFold3🚀
A set of libraries for aligning, profiling, and predicting the structure of proteins
A deep learning method that identifies improved protein conformational states in trajectory data from refinement simulations
Macromolecule structure modeling from cryo-EM maps
Recurrent neural network implementations for protein secondary structure prediction and language models
AI-agent toolkit for structural biology: design binders, map structures, screen candidates, rank results, and prepare cloud-scale runs.
A Snakemake workflow for high-throughput AlphaFold 3 structure predictions
A modular, extensible peptide design pipeline with target preparation, backbone generation, sequence design, scoring, and ranking. Full local CPU pipeline, and backend hooks for RFpeptides, ProteinMPNN/LigandMPNN, and ColabFold.
Predict the whole sequence and 3D structure of masked protein sequences with ESM by @evolutionaryscale
Structure-aware functional annotation of phage genomes.
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