Protein function annotation with maximally spanning representations

Code for ICLR 2024 (Spotlight) paper "MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding"

No fortress, purely open ground. OpenManus is Coming.

Gymnasium framework for training language model agents on constructive tasks

Metrics for our protein design competitions.

Protein stability prediction using rewired protein generative models

Code for ICML2020 paper - CLUB: A Contrastive Log-ratio Upper Bound of Mutual Information

Tools for the generation, analysis and visualisation of complex networks in hyperbolic space.

Examples for https://github.com/optuna/optuna

Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

BioLiP2 database curation and web interface

COSMIS is a framework for quantifying the mutational constraint on amino acid sites in 3D spatial neighborhoods. The framework currently maps the landscape of 3D mutational constraint on 6.1 amino …

Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders

Multi-task and masked language model-based protein sequence embedding models.

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

Connect the dots in networks.

This is an official implementation for "MMSite: A Multi-modal Framework for the Identification of Active Sites in Proteins".

Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data

AlphaFold 3 inference pipeline.

ColabFold on your local PC

Making Protein folding accessible to all!

User friendly and accurate binder design pipeline