Gen-COMPAS
https://github.com/Tangcyu/Gen-COMPAS
Few-step Cofolding with All-Atom Flow Maps
https://arxiv.org/abs/2606.08375
The fastest open-source foundation model for DNA
https://huggingface.co/spaces/HuggingFaceBio/carbon-demo
Mechanisms of AI Protein Folding in ESMFold
https://folding.baulab.info/
Teaching AI to Invent Enzymes Nature Never Imagined
https://disco-design.github.io/
BioReason-Pro: Advancing Protein Function Prediction with Multimodal Biological Reasoning
https://github.com/bowang-lab/BioReason-Pro
Feynman-Kac steering for controllable protein diffusion
https://github.com/ErikHartman/FK-RFdiffusion
Co-designing sequence and structure of functional de novo
enzymes with EnzyGen2
https://www.biorxiv.org/content/10.64898/2026.03.02.709205v2.full.pdf
AI protein design for everyone
https://evedesign.bio/
CellVoyager
https://github.com/zou-group/CellVoyager
Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute
https://github.com/NVIDIA-Digital-Bio/Proteina-Complexa
ProteinEBM
https://github.com/jproney/ProteinEBM
Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles
https://www.biorxiv.org/content/10.64898/2026.03.02.708991v2
PerturbGen predicts how gene perturbations reshape cell fate across development, disease, and engineered systems
https://cellatlas.io/perturbgen#datasets
Hematopoiesis Manifold Viewer
https://biodyn-ai.github.io/hema-manifold/
LabClaw – Skill Operating Layer for Stanford LabOS & Next-Gen AI Co-Scientists
https://github.com/wu-yc/LabClaw
BAGEL: Protein Engineering via Exploration of an Energy Landscape
https://github.com/softnanolab/bagel
Protein Diffusion Models as Statistical Potentials
https://github.com/AI-Universeity/AI-Track
AlphaGenome Research
https://github.com/google-deepmind/alphagenome_research
Training a discrete diffusion model on biological sequences
https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_tutorials/06_NTv3_generative_training.ipynb
squidiff: Predicting cellular development and responses to perturbations using a diffusion model
https://github.com/siyuh/Squidiff
SeedFold: Scaling Biomolecular Structure Prediction
https://arxiv.org/abs/2512.24354
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants
https://www.nature.com/articles/s41587-024-02511-w
Protein design with Foundry
https://github.com/RosettaCommons/foundry
BoltzGen: Toward Universal Binder Design
https://boltz.bio/boltzgen
OpenFold3-preview
https://github.com/aqlaboratory/openfold-3
Umol - Universal molecular framework
https://github.com/patrickbryant1/Umol
Cell2Sentence: Teaching Large Language Models the Language of Biology
https://github.com/vandijklab/cell2sentence
Let Physics Guide Your Protein Flows: Topology-aware Unfolding and Generation
https://arxiv.org/abs/2509.25379v1
ProT-VAE: Protein Transformer Variational AutoEncoder for functional protein design
https://www.pnas.org/doi/10.1073/pnas.2408737122
Enzyme specificity prediction using cross attention graph neural networks
https://www.nature.com/articles/s41586-025-09697-2
Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamics
https://arxiv.org/abs/2510.07589
Open-Source Neural Networks for Biomolecular Tasks
https://github.com/RosettaCommons/modelforge
How to go with the flow: flow matching in bioinformatics and computational biology
https://amorehead.github.io/assets/pdf/How_to_go_with_the_flow__flow_matching_in_bioinformatics_and_computational_biology.pdf
Molecular Simulations: The Fun Way to Predict Binding Affinity
https://blog.litefold.ai/mds
SO3krates and Universal Pairwise Force Field for Molecular Simulation
https://github.com/general-molecular-simulations/so3lr