TPepPro: a deep learning model for predicting peptide-protein interactions

Molecular dynamics simulations with an LLM agent

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications

Draw datasets from within Python notebooks.

Official repository for Target-Specific De Novo Peptide Binder Design with DiffPepBuilder

Python tool for converting files and office documents to Markdown.

Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction (CASP16)

Inference code for PoET: A generative model of protein families as sequences-of-sequences

Fully automated high-throughput MD pipeline

Making Protein Design accessible to all via Google Colab!

Official repository for the Boltz-1 biomolecular interaction model

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/

In silico directed evolution of peptide binders with AlphaFold

An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

User friendly and accurate binder design pipeline

AutoDock Vina

Shapley Interactions and Shapley Values for Machine Learning

Publication-quality network visualisations in python

Training neural network potentials

OpenMM plugin to define forces with neural networks

A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.

End-To-End Molecular Dynamics (MD) Engine using PyTorch

Deep learning framework for proteomics

Peptide level annotation for proteomics datasets