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Starred repositories
Official code implementation for NEURAL SPACETIMES FOR DAG REPRESENTATION LEARNING
Interaction Fingerprints for protein-ligand complexes and more
Molecular Descriptors with Actively Identified Subsets
Official code release for paper "Temporal Score Rescaling for Temperature Sampling in Diffusion and Flow Models"
Code and data to explore neural scaling laws of xLSTM and Transformer models.
Humanness of de-novo designed proteins
Sapiens is a human antibody language model based on BERT.
BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody se…
GatorAffinity: Boosting Protein-Ligand Binding Affinity Prediction with Large-Scale Synthetic Structural Data
Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders
Collection of scripts to perform benchmarking.
TorchCFM: a Conditional Flow Matching library
mBER - Manifold Binder Engineering and Refinement. mBER enables antibody binder design by leveraging structure templates and sequence conditioning in backprop design through AlphaFold-Multimer. Pre…
A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS
MiniFold: Simple, Fast and Accurate Protein Structure Prediction
A Euclidean diffusion model for structure-based drug design.
ShinkaEvolve: Towards Open-Ended and Sample-Efficient Program Evolution
Annotated implementations of equivariant (graph) neural networks in Jax: EGNN, SEGNN, NequIP.
Codebase for Germinal, a broadly enabling generative pipeline for efficient generation of epitope-targeted de novo antibodies.
Official repository for "Energy Matching: Unifying Flow Matching and Energy-Based Models for Generative Modeling" [NeurIPS 2025]
enumerate a large amount of rdkit valid SMILES.
Official source code of HELM, a family of fully hyperbolic large language models
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
A single-page application to extract references from academic papers by DOI, convert them to various citation formats, and download them in bulk.