A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.

PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

Clusters protein chains based on CA distance difference

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.

Automated generation of immunogenic peptides from protein structures and molecular docking analysis using AlphaFold2 and AutodockVina.

BioStructures Image Database and Experiments Schema

ProteinInteractionFinder (PIF) is a Java 11 library for determining interatomic interactions in protein structures, obtained from PDB (Protein Data Bank) files.

Diffusion Kernel-based Graph Node Clustering for Protein Domain Assignment

The official repository of the Nexus Resonance Codex (NRC)

Find all PDB structures associated with a UniProt entry. #Haku

Identify residue contacts shared across all or most protein structures of a give protein family

Yale Gradute School module CBB752 final group project by Jiaqi Li, Keyi Li, and Anna Su.

List the protein chains and ligands in structural file(s). #Haku