Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..
Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..
Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)
AI-native tensor format (.ptt) for protein-structure ML. Convert a structure or sequence once; load backbone, MSA, ESM embeddings, sparse pair features, and ligands with zero parsing. Feeds AlphaFold/Boltz (Boltz-2 verified). Zarr-backed, lossless, PyTorch/JAX-ready, streams from S3/GCS.
A high-performance, pure Rust library for full-atom protein side-chain packing using the DREIDING force field, Goldstein+Split DEE, and tree-decomposition DP—with native protein–ligand and protein–nucleic acid interface support.