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ChatPDB
Protein Structure Visualization Assistant
LLMRAGPyMOLFastAPIVector DBPython
An intelligent assistant that interprets natural language queries to visualize
3D protein structures from the RCSB PDB. Integrates LLMs with a RAG pipeline
for semantic understanding of protein documentation, and PyMOL for interactive
rendering — enabling biomedical researchers to query structural data
conversationally without writing visualization scripts.
System Architecture
User Query
natural language
↓
LLM Parsing
intent & entity extraction
↓
Vector Retrieval
protein metadata & docs
↓
PyMOL Generation
command synthesis
↓
3D Visualization
interactive output