Protein SMILES and SMARTS

• Treat proteins as big organic molecules. Use SMILES and SMARTS
• Create TDT of Protein Data Base
• Create protein smiles. Find chains and parts
• Derive actual protein sequences
• Find ligands and assign connectivity
• Parse textual information and add to TDTs
• Creates a ~4GB TDT file
• Use SMARTS to find features.
  • Patterns in SEA language to assign interactions
  • SMARTS based rules to assign constraints for PLAID layout