QRNAS: Quick Refinement of Nucleic Acid Structures

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

A diffusion-based ML model for de novo design of DNA, RNA, proteins, and mixed assemblies.

WeDLM: The fastest diffusion language model with standard causal attention and native KV cache compatibility, delivering real speedups over vLLM-optimized baselines.

A character-level language diffusion model trained on Tiny Shakespeare

Fast numerical array expression evaluator for Python, NumPy, Pandas, PyTables and more

A optimized PyTorch framework for behavior cloning with flow related generative models.

Official Implementation of AMix-1, a Test-Time Scalable Protein Language Model.

Code for running RFjoint2

Source code for CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs

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

[NeurIPS 2025 Spotlight] E2Former: An Efficient and Equivariant Transformer with Linear-Scaling Tensor Products

a differentiable forcefield based on FoldX built in pytorch

A unified framework for machine learning collective variables for enhanced sampling simulations

[NeurIPS 2025] Implementation for the paper "The Surprising Effectiveness of Negative Reinforcement in LLM Reasoning"

PeptoneBench: evaluating protein ensembles across the order-disorder continuum

Official code release for Ambient Protein Diffusion

Machine Learning tools for Coarse Graining

Potts model-based protein sequence design

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

Rapid Generation of Rare Event Pathways Using Direction Guided Adaptive Sampling: From Ligand Unbinding to Protein (Un)Folding

Profluent-E1 family of Protein Encoder Models