The structure database used by SWISS-MODEL is derived from the Protein Data Bank (PDB). In order to allow rapid retrieval of the relevent structral information, each protein chain of the database was placed in an individual file.

The ExPDB codes are constructed according to the following rule:

PDBCODE+ChainID

Examples:

LIGHT HARVESTING PROTEIN : 1CPC

two chains (with IDs A & B) in the following entries

• Chain A: 1CPCA
• Chain B: 1CPCB

one chain (without chain ID), the corresponding ExPDBentry:

• 1MAL_

Sequence Database: ExNRL-3D

A sequence database, reflecting the protein sequences of ExPDB is used by BLAST to search for suitable modelling templates. Residues with structural modifications (HYP,PCA,SEP,MSE etc.) are replaced by their genetic precursors (i.e. PRO,GLU,SER,MET etc.).