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1. protein-classify-and-cluster protein-classify-and-cluster Public

   A Python pipeline for protein structure clustering (PDBs) using all-vs-all TMalign, hierarchical analysis, and secondary structure classification.

   Python 5 2

2. find_interface_hotspot find_interface_hotspot Public

   interface-hotspot finder for RFdiffusion PPI binder design using gemmi + distance-based contact scoring with residue-type weighting and optional exclusions.

   Python 2 1

3. partial-diffusion-in-batch partial-diffusion-in-batch Public

   Python implementation of partial-diffusion-in-batch: efficient batch-wise partial diffusion methods for accelerating diffusion model training and inference.

   Python 2 1

4. alphafold3-protein-screening alphafold3-protein-screening Public

   A lightweight CLI tool to scan AlphaFold 3 outputs, aggregate confidence metrics into a single table, filter by user-defined thresholds, and export top-ranked structures.

   Python 5 1

5. DuoForge-Ab DuoForge-Ab Public

   An easy-to-use de novo antigen design pipline, combines the sota models in each steps

   Python 1 1

6. Molecule-Strcture-Extractor Molecule-Strcture-Extractor Public

   Batch extraction of protein-only targets from protein–nucleic-acid PDB/mmCIF complexes.

   Python 1