OVO, an open-source ecosystem for de novo protein design
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May 29, 2026 - Python
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rfdiffusion
Here are 20 public repositories matching this topic...
Official repository for the ProteinDJ protein design pipeline
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Mar 26, 2026 - Python
A Nextflow pipeline for protein binder design
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Jun 6, 2026 - Python
A modular, extensible peptide design pipeline with target preparation, backbone generation, sequence design, scoring, and ranking. Full local CPU pipeline, and backend hooks for RFpeptides, ProteinMPNN/LigandMPNN, and ColabFold.
machine-learning bioinformatics computational-biology drug-discovery structure-prediction alphafold colabfold peptide-design rfdiffusion proteinmpnn
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Nov 28, 2025 - Python
De novo design of a miniprotein binder targeting the SARS-CoV-2 spike RBD using RFdiffusion, ProteinMPNN, and Rosetta. A step-by-step project integrating generative AI and structural bioinformatics.
drug-discovery protein-design structural-bioinformatics generative-ai rfdiffusion miniprotein-binder-rfdiffusion
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Aug 11, 2025 - Python
Protein binder design GUI
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Apr 13, 2026 - Python
RNA-seq counts to ranked de novo protein binder candidates, with full provenance back to the patient cohort.
bioinformatics rna-seq computational-biology reproducibility prov-o protein-design streamlit alphafold ro-crate boltz rfdiffusion proteinmpnn de-novo-binder-design
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Jun 4, 2026 - Python
Manage protein design processes
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Apr 13, 2026 - Shell
구조 기반 de novo 항체 설계
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Aug 6, 2025 - Python
Personalized lymphoma therapy design with Gemma 4, AlphaFold, RFdiffusion. Kaggle Gemma 4 Good Hackathon submission.
gemma oncology personalized-medicine bcr car-t alphafold lymphoma antibody-design rfdiffusion proteinmpnn kaggle-hackathon idiotype
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May 5, 2026 - Python
De novo protein binder design pipeline: motif-scaffolded RFdiffusion + ProteinMPNN + AlphaFold2 self-consistency validation. PD-L1 reference example.
bioinformatics structural-biology computational-biology drug-discovery protein-design generative-models diffusion-models alphafold rfdiffusion proteinmpnn
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Apr 28, 2026 - Python
Design proteins in your terminal. A TUI agent for de novo protein design — free by default.
go bioinformatics tui protein-design de-novo-design bubble-tea alphafold vllm llm-agent ollama rfdiffusion proteinmpnn
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May 26, 2026 - Go
Cross-Model CKA: EVO2/FAESM–RFdiffusion3 alignment reflects low-frequency smoothing bias, not structural convergence. Paper + full analysis pipeline.
machine-learning protein-structure computational-biology representation-learning esm interpretability cka rfdiffusion dna-language-model
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May 9, 2026 - Python
Molecular dynamic simulation of RFdiffusion/ProteinMPNN designed HMERF mutated titin Ig152/Fn3-119 domain protein binder
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Feb 18, 2026 - Python
🧬 Lectures for course ML-protein-design
tensorflow pytorch biopython pymol rdkit modeller pytorch-geometric deepchem alphafold2 py3dmol colabfold rfdesign pyfoldx molgan trdesign rfdiffusion proteinmpnn colabdesign dmasif
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Dec 17, 2024 - Jupyter Notebook
UC Berkeley MSSE Capstone Project: Evaluating & refining filtering strategies for de novo protein binders
protein-structure filtering protein-design protein-protein-interaction protein-folding protein-binding denovo-design protein-expression binding-prediction rfdiffusion boltz2
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May 13, 2026 - Jupyter Notebook
Universal Peptide Drug Discovery — AI-driven cyclic peptide design pipeline with ncAA integration
dft molecular-dynamics openmm computational-chemistry drug-discovery protein-design qmmm binding-free-energy alphafold2 peptide-design rfdiffusion proteinmpnn cyclic-peptide non-canonical-amino-acids
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May 29, 2026 - Python
🧬 Experiments and setup of RFdiffusion/ProteinMPNN running on macOS Apple Silicon (CPU).
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Dec 31, 2025 - Python
Protein binder design targeting the PCNA PIP site using RFdiffusion, ProteinMPNN, and AlphaFold
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May 29, 2026 - Jupyter Notebook
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