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1. HelixDB HelixDB Public

   AI-native tensor format (.ptt) for protein structure ML. Convert mmCIF/PDB structures or raw sequences once, then load backbone, MSA, embeddings, and bond graphs in milliseconds. Feeds AlphaFold/Bo…

   Python

2. lacuna lacuna Public

   Find cryptic binding pockets that single-structure tools miss. Generates a conformational ensemble from any PDB/mmCIF and ranks transiently-open, druggable sites. Pure Python, no GPU.

   Python

3. google-deepmind/alphafold3 google-deepmind/alphafold3 Public

   AlphaFold 3 inference pipeline.

   Python 8.2k 1.3k

4. jwohlwend/boltz jwohlwend/boltz Public

   Official repository for the Boltz biomolecular interaction models

   Python 4.1k 847

5. NVIDIA-BioNeMo/nvMolKit NVIDIA-BioNeMo/nvMolKit Public

   A high-performance, GPU-accelerated library for key computational chemistry tasks, such as molecular similarity, conformer generation, and geometry relaxation.

   Cuda 260 25

6. rowansci/openconf rowansci/openconf Public

   Python 67 6