User friendly and accurate binder design pipeline
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Sep 21, 2026 - Jupyter Notebook
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pyrosetta
Here are 15 public repositories matching this topic...
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
jupyter-notebook dna rosetta rna-structure-prediction protein-design protein-folding protein-structure-prediction google-colab pyrosetta protein-docking
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Sep 19, 2026 - Jupyter Notebook
Automated, modular pipeline for de novo protein binder design on SLURM clusters, with the BFmonitor dashboard
deep-learning structural-biology slurm protein-design pyrosetta alphafold2 de-novo-protein-design rfdiffusion proteinmpnn protein-binders cnio
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Sep 23, 2026 - Python
RosettaDesign using PyRosetta
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Aug 22, 2019 - Python
Using Rotamer Interaction Fields from RIFGen/Dock in python
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May 2, 2021 - Python
Protein Structure prediction using Hybrid Differential Evolution (HybridDE)
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Apr 23, 2021 - Python
A Rosetta-based Python tool for constructing user-defined variant libraries with amino acid insertions, deletions, using loop closure algorithms and energy minimization.
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Jan 17, 2025 - Python
Pre-registered self-consistency benchmark of ProteinMPNN VHH redesigns (PDB 8YVJ): ESMFold/AF2-multimer refolding + Rosetta interface cross-check, with shuffle/random/native controls
reproducible-research structural-biology computational-biology pymol drug-discovery protein-design inverse-folding pyrosetta alphafold nanobody esmfold proteinmpnn antibody-engineering
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Nov 5, 2026 - Jupyter Notebook
Does RFdiffusion hotspot specification change binder design outcomes? 50 epitope vs 50 non-epitope control designs, judged against pre-registered criteria. The generator's own backbones show no difference (0.93×); independent AF2 re-prediction shows 12.0×.
structural-biology computational-biology protein-design protein-protein-interaction preregistration pd-l1 pyrosetta alphafold2 rfdiffusion proteinmpnn
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Nov 5, 2026 - Jupyter Notebook
Method-independent benchmark of five de novo protein binder design tools on HPC
benchmark bioinformatics molecular-dynamics bioinformatics-pipeline gromacs protein-design pyrosetta bindcraft rfdiffusion boltzgen
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Sep 9, 2026 - Python
Structural bioinformatics pipeline for clustering antibody-antigen epitopes by geometric similarity and deriving consensus paratope design constraints for antibody engineering.
clustering protein-design structural-bioinformatics immunoinformatics antibodies protein-engineering pyrosetta epitope paratope sabdab
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Sep 27, 2026 - Python
Computes biophysical metrics from monomeric PDB structures for use as features in machine learning models.
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Aug 1, 2026 - C++
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