AAindexNC

AAindexNC estimates the physicochemical properties of non-canonical amino acids derived from protein structures and the PDBechem databank, extending the AAindex database to support predictive modeling of protein structures and properties.

Key Features:

• Non-canonical amino acid property estimation: Evaluates physicochemical properties from the AAindex database for non-canonical amino acids not covered by the original 20 canonical amino acids.
• SMILES-based chemical composition: Uses SMILES encoding obtained from the PDBechem databank to represent chemical composition of non-canonical amino acids from the PDB.
• Prediction quality assessment: Assesses the quality of predicted physicochemical properties for non-canonical amino acids.
• Database expansion: Builds upon the existing AAindex database to include estimated properties for more than 1000 distinct non-canonical amino acids found in the Protein Data Bank.

Scientific Applications:

• Protein structure prediction: Provides physicochemical property predictors for building models to predict protein structures using non-canonical amino acid data.
• Protein property prediction: Enables prediction of protein properties by supplying physicochemical parameters for non-canonical amino acid residues.
• Non-canonical amino acid analysis: Supports computational studies of proteins containing non-canonical amino acids deposited in the Protein Data Bank.

Methodology:

The method uses SMILES encoding from the PDBechem databank to represent chemical composition of non-canonical amino acids from the PDB, then evaluates physicochemical properties from the AAindex database for these non-canonical amino acids.