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HADDOCK Scriptorium - Producing restraints for gapped structures

Some protein structures are not determined at sufficient resolution to discern all the residues in the density map. Alternatively, very flexible regions of a peptide chain cannot be determined trivially by x-ray crystallography. Finally, structures such as those of antibody molecules are composed of several chains that must keep a particular structure throughout the computational simulation in order to have a biological meaning.

The script here deposited identifies gaps in structures and produces suitable distance constraints that prevent unnatural deformations of the peptide chain(s). The gaps can be of two types, although these are merely informative, as they are treated in the same manner:

  • Sequence Gaps: whenever there is a break in the residue numbering in the PDB file, eg. 1,2,5,6,...
  • Distance Gaps: whenever the alpha carbons of two adjacent residues are located further than a certain distance threshold in Ångstrom (default, 4Å).

The script is written in Python and requires no additional dependencies. Use it by simply calling it with the structure you wish to be checked as the first argument (structure.pdb in the following example):

python gap_check.py structure.pdb
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