A Nextflow pipeline for protein binder design
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May 28, 2026 - Python
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proteinmpnn
Here are 21 public repositories matching this topic...
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
Open hotspot-guided de novo protein binder design pipeline integrating OpenMM, BindCraft, ProteinMPNN, and AlphaFold2.
computational-biology structural-bioinformatics immuno-oncology protein-protein-interactions alphafold2 contact-maps de-novo-protein-design bindcraft proteinmpnn protein-binder-design hotspot-mapping oncogenic-interfaces
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Apr 16, 2026 - Jupyter Notebook
Protein binder design GUI
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Apr 13, 2026 - Python
Unified Python library and CLI for protein structure prediction and inverse folding.
python cli bioinformatics deep-learning structural-biology transformers computational-biology pytorch protein-design inverse-folding protein-structure-prediction alphafold2 alphafold-multimer directed-evolution esmfold esm2 esm-if proteinmpnn ligandmpnn ai4protein
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Feb 16, 2026 - Python
Retraining of ProteinMPNN model specifically with acid-stable structures and sequences
protein-stability protein-design inverse-folding protein-engineering proteinmpnn acidophile protein-ph-stability
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May 13, 2026
LigandMPNN but with dynamic constraints. This allows the biases applied during inference to adjust to a desired goal during the generation process. Current implementations are for pI targeting and surface patch generation
protein-structure protein protein-design inverse-folding protein-engineering proteinmpnn protein-electrostatics
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Apr 22, 2026 - Python
Protein binder mutagenesis GUI
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Apr 21, 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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May 27, 2026 - Python
Optimized ProteinMPNN for Apple Silicon: 15× speedup with 0% accuracy loss through architecture pruning, batching, and ANE acceleration. Comprehensive benchmarking study of speed-accuracy trade-offs.
benchmark machine-learning bioinformatics deep-learning computational-biology pytorch protein-design mlx coreml protein-engineering graph-neural-networks model-optimization neural-engine apple-silicon proteinmpnn
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Feb 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
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
Manage protein design processes
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Apr 13, 2026 - Shell
PEN-ASSEMBLE: Automated Strategy and Scoring Engine for Molecular Bridge-recombinase Library Engineering | IS110-family design pipeline, 1,029 candidates, 5/5 pre-registered predictions | Part of PEN-STACK
python bioinformatics synthetic-biology computational-biology protein-design genome-editing genetic-engineering gene-therapy pen-stack proteinmpnn genome-atlas bridge-recombinase is110-family penscore deimmunization mech-class
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May 26, 2026 - HTML
Computational pipeline for measuring protein interior reprogrammability. Identifies chassis candidates where exterior fold is preserved while interior chemistry varies.
bioinformatics ai enzyme synthetic-biology computational-biology protein protein-design enzyme-testing protein-engineering protein-folding alphafold proteinmpnn
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Mar 16, 2026 - Shell
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
🧬 Experiments and setup of RFdiffusion/ProteinMPNN running on macOS Apple Silicon (CPU).
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Dec 31, 2025 - Python
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 28, 2026 - Python
Empirical dual-use risk assessment of protein language models (ESM-2) and structure-based design tools (ProteinMPNN)
evaluation ai-safety biosecurity protein-language-model foundation-models biosafety evodiff esm-2 dual-use proteinmpnn ligandmpnn
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May 25, 2026 - Python
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