Stars
This is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.
This repository contains all the input files used for the L-ABF-OPES paper: "L-ABF-OPES: Absolute Binding Free Energy Calculations Using Local Adaptively Biased Force and On-the-Fly Probability Enh…
ECloudGen: Leverage Quantum Physics to Scale Chemical Space for Structure-based Molecular Design
Nature Methods: RNA foundation model (together with RhoFold)
Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning
IntelliFold: A Controllable Foundation Model for General and Specialized Biomolecular Structure Prediction.
CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions (KDD'25 research track accepted)
State is a machine learning model that predicts cellular perturbation response across diverse contexts
(Windows) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
GNN trained to predict changes in thermodynamic stability for protein point mutants
an efficient distributed PyTorch framework
Official Repository for the Uni-Mol Series Methods
Refactored for Compatibility with Amber20
FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery
PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.
[IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models
Scripts for virtual screening, cross docking and protein relax using Schrödinegr and Rosetta
Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python
DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models
Weighted Ensemble simulation framework in Python
Workflow to clean up and fix structural problems in protein-ligand binding datasets
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361