RINGER: Rapid Conformer Generation for Macrocycles with Sequence-Conditioned Internal Coordinate Diffusion

A Multi-Task Generative model for Structure-Based Drug Design

KinDEL is a large DNA-encoded library dataset containing two kinase targets (DDR1 and MAPK14) for benchmarking machine learning models.

Shotgun approch for modeling of POI-PROTAC-E3 ternary complex.

Implementation for SuperWater

A tool for retrosynthetic planning

Template-based protein-ligand pose prediction with web interface.

Data-driven generation of conformational ensembles and ternary complexes for PROTAC and other Chimera systems

Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning

Electron-density-informed effective and reliable de novo molecular design and optimization with ED2Mol

LoQI: Low Energy QM Informed Conformer Generation

Efficient Sampling of PROTAC-Induced Ternary Complexes

Central repository for biomolecular foundation models with shared trainers and pipeline components

Megalodon

Conversion of PDBx/mmCIF files to best effort/minimal PDB files

ML-guided visual inspection for molecular docking

SBDD Benchmarking

Implementation of SCINS

Official implementation of RuSH (Scaffold Hopping with Generative Reinforcement Learning). Includes ScaffoldFinder algorithm for 2D decoration identification, 3D shape-based scoring with ROCS, and …

A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.

Physics-Guided All-Atom Diffusion Model for Accurate Protein-Ligand Complex Prediction

Official Implementation of "What Ails Generative Structure-based Drug Design: Too Little or Too Much Expressivity?", published at AISTATS 2025 (oral)

MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation

The official implementation of DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design (ICML 2023)