Implementation for SE(3) diffusion model with application to protein backbone generation

A Euclidean diffusion model for structure-based drug design.

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

Code of “Multi-Modal Deep Learning Enables Ultrafast and Accurate Annotation of Enzymatic Active Sites”

Structure prediction of alternative protein conformations

Collecting research materials on EBM/EBL (Energy Based Models, Energy Based Learning)

A deep neural network with hybrid architecture (EGNN + Transformer) for molecular properties prediction.

[ICLR'24 spotlight] Saprot: Protein Language Model with Structural Alphabet

Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation

Public RFDiffusionAA repo

Learning in infinite dimension with neural operators.

CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes

Topological transformer for protein-ligand complex interaction prediction.

PSICHIC (pronounced Psychic) - PhySIcoCHemICal graph neural network for learning protein-ligand interaction fingerprints from sequence data

A physical property evaluation toolkit from the Open Forcefield Consortium.

Treeffuser is an easy-to-use package for probabilistic prediction on tabular data with tree-based diffusion models.

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

Graphormer is a general-purpose deep learning backbone for molecular modeling.

Predicting tandem mass spectra from molecules

Machine learning predictions of bond dissociation energy

A graph neural network for the prediction of bond dissociation energies for molecules of any charge.