#structural-biology

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

A lightweight Python library for simulating Small-Angle X-ray Scattering (SAXS) profiles from protein coordinates, with Jupyter Notebook examples.

Yet another version of PDBx/mmCIF Python implementation

Differentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.

NMR spectroscopy calculations for protein structures. Jupyter Notebook tutorials are available to visualize the concepts.

A Julia package to read, write and manipulate macromolecular structures

An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

Generate restraints to be used in HADDOCK

A Rust library for parsing PDB (Protein Data Bank) files

Identifies relevant ligands in the PDB

Differentiable VAE framework for predicting protein structural ensembles (IDPs) consistent with SAXS and NMR data. Built on JAX/Flax.

JAX-native differentiable protein folding framework integrating experimental NMR constraints (RDCs) and biophysical "self-correction." Several Jupyter Notebooks visualize the concepts.

Real-time VSCode extension and standalone Python script for validating mmCIF/CIF files against the PDBx/mmCIF dictionary or any CIF dictionary.

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.

Generate realistic synthetic 3D Cryo-EM densities from structural models for testing algorithms and training ML models.

Build a Mine-schema database from PDB data. Load PDBj structural biology data into PostgreSQL with RDKit chemical search support.

This application is designed to create mmcif files from facilities data.