Database Access Nodes
Access to major chemical and biological databases including PubChem and RCSB PDB for comprehensive compound and structure retrieval.
Node Reference
Detailed documentation for each database access node available in VERA.
PubChem Search
Search PubChem database for chemical compounds and retrieve molecular data
Key Features
- •Multiple search types (name, SMILES, CID, CAS)
- •Batch compound retrieval
- •Property data extraction
- •3D structure download
- •Synonym and identifier lookup
- •Error handling and retry logic
Input Ports
Search query (name, SMILES, CAS, etc.)
Search type (name, smiles, cid, etc.)
Output Ports
Found molecular structures
Compound metadata and properties
Search results summary
RCSB PDB Search
Search RCSB Protein Data Bank for protein structures
Key Features
- •Advanced query capabilities
- •Structure and sequence search
- •Ligand-bound structure filtering
- •Resolution and quality filters
- •Bulk download support
- •Metadata extraction
Input Ports
PDB search query
Search type (protein, ligand, etc.)
Output Ports
Retrieved protein structures
PDB entry metadata
Search results overview
Workflow Examples
Common database integration workflows for research and drug discovery.
Drug Discovery Pipeline
Search for compounds and screen against protein targets
- 1Search PubChem for compounds with specific properties
- 2Download 3D structures from RCSB PDB
- 3Filter compounds by drug-likeness criteria
- 4Prepare structures for molecular docking
- 5Run virtual screening with AutoDock Vina
- 6Analyze docking results and select hits
Target Identification
Find protein targets for compounds of interest
- 1Search PubChem for compounds of interest
- 2Find co-crystallized structures in RCSB PDB
- 3Extract protein-ligand interaction data
- 4Identify key binding residues
- 5Analyze binding pocket characteristics
- 6Generate target validation data
Supported Databases
Integration with major chemical and biological databases for comprehensive data access.
PubChem
The world's largest collection of freely accessible chemical information
- • 110+ million compounds
- • Chemical structures and properties
- • Biological activities
- • Literature references
RCSB PDB
Protein Data Bank with 3D structural data for biological molecules
- • 190,000+ structures
- • Protein and nucleic acid structures
- • Small molecule ligands
- • Experimental metadata