Deep neural models for core NLP tasks (Pytorch version)

An implementation of the DeepMind's AlphaFold based on PyTorch for research

Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

Protein Secondary Structure predictor using Convolutional Neural Networks

A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)

nucleic acid folding

Python bindings for the `buildcell` program for Ab Initio Random Structure Searching (AIRSS)

[ACL 2023] SPEECH: Structured Prediction with Energy-Based Event-Centric Hyperspheres

Your open-source alternative to AlphaFold3🚀

Active Imitation Learing with Noisy Guidance

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

Recurrent neural network implementations for protein secondary structure prediction and language models

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.

Predict the whole sequence and 3D structure of masked protein sequences with ESM by @evolutionaryscale

A Snakemake workflow for high-throughput AlphaFold 3 structure predictions

Computing descriptors for AIRSS style SHELX files.

An implementation of a genetic algorithm in Python for predicting equilibrium crystal structures for a given potential. The potential implemented here is the Daoud-Cotton model, but this can be easily changed.

methods used to design binders for BioML Challenge 2024 - hCD20 target

Searching proteins against a database of embeddings