Making Protein folding accessible to all!

Deep neural models for core NLP tasks (Pytorch version)

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

Evolutionary couplings from protein and RNA sequence alignments

Comprehensive benchmarking of protein-ligand structure prediction methods. (Nature Machine Intelligence)

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

[EMNLP 2022] Generative Knowledge Graph Construction: A Review

Protein Secondary Structure predictor using Convolutional Neural Networks

nucleic acid folding

This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202

PSP is a python toolkit for predicting atomic-level structural models for a range of polymer geometries.

Visualize the inner workings of RNA bioinformatics algorithms for structure prediction, interaction prediction and sequence alignment.

RNAGenesis: A Generalist Foundation Model for Functional RNA Therapeutics

RNA secondary structure prediction tool

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

Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.

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.

Code repository for the SPOC tool for scoring binary AF-M predicitons.

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

deep learning based prediction of structures and functional groups from MS/MS spectra

POC Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction

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

[ACL'23 main] DICE: Data-Efficient Clinical Event Extraction with Generative Models

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

A pipeline for AlphaFold2-Multimer on a SLURM compute cluster with visualization in ChimeraX.

A Snakemake workflow for high-throughput AlphaFold 3 structure predictions