atomic coordinates according to the X-ray structure of the protein.
To illustrate the notion, we use the 1EEI.pdb file, which is the
crystallographic version of the Cholera Toxin (see [13]).
The Cholera Toxin is composed by 5 identical chains and the
whole protein has a cyclic shape (Fig. 2).
Nevertheless, the whole study is done using a data set of
750 oligomeric proteins from 2 up to 20 chains (Fig. 3).
For each protein, we take the associated PDB file and we
consider all the atoms and their spatial positions in the three
dimensional space given in Angstroms. The Adjacent Amino Acid
Fig. 1 Screenshot of one page of the Protein Data Bank
Fig. 2 Cyclic shape of the cholera toxin
116
Claire Lesieur and Laurent Vuillon
To illustrate the notion, we use the 1EEI.pdb file, which is the
crystallographic version of the Cholera Toxin (see [13]).
The Cholera Toxin is composed by 5 identical chains and the
whole protein has a cyclic shape (Fig. 2).
Nevertheless, the whole study is done using a data set of
750 oligomeric proteins from 2 up to 20 chains (Fig. 3).
For each protein, we take the associated PDB file and we
consider all the atoms and their spatial positions in the three
dimensional space given in Angstroms. The Adjacent Amino Acid
Fig. 1 Screenshot of one page of the Protein Data Bank
Fig. 2 Cyclic shape of the cholera toxin
116
Claire Lesieur and Laurent Vuillon