Suns

Suns provides real-time all-atom structural search and native-like fragment retrieval from the Protein Data Bank (PDB) to support atomic-level queries for protein design within PyMOL.

Key Features:

• Real-Time Atomic Search: Constructs detailed atomic-level search queries and streams aligned search results within seconds.
• All-Atom Fragment Retrieval: Performs all-atom searches to retrieve native-like fragments and structural motifs from PDB entries.
• Integration with PyMOL: Integrates a search engine into PyMOL to execute atomic-level structural queries within the visualization environment.
• Designability-Inspired Approach: Enables searching for and incorporation of tertiary interactions and motifs from existing proteins to identify scaffolds compatible with specified hot-spot residues.
• Architecture: Includes a command-line client and a server-side search engine for query execution and result delivery.
• Data Source: Uses structural data from the Protein Data Bank (PDB) as the repository for search targets.

Scientific Applications:

• De Novo Protein Design: Supports design of novel proteins by retrieving and reusing native-like structural templates from the PDB.
• Structural Motif Identification: Identifies and extracts specific protein motifs for incorporation into new designs.
• Tertiary Interaction Exploration: Aids analysis and design of complex tertiary interactions important for protein stability and function.
• Scaffold Identification for Hot-Spot Residues: Finds scaffolds compatible with critical residues to support functional design objectives.

Methodology:

Suns integrates a server-side all-atom search engine with a command-line client and a PyMOL interface to perform atomic-level structural queries against PDB entries and stream aligned search results.