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Missing residues, including those with occupancy equal to zero, were treated as disordered.
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The initial dataset of loops is further filtered by a quality rule: no loops were considered with missing residues or missing main chain atoms (including Cβ, except for Glycine).
To complete the missing residues, e.g., the first three amino acids in calmodulin PDB structure 1CLL, the build-residue function in PyMOL software is used.
Possible steps include: choice of the specific model number if several are available in a single PDB entry or which PDB entry if multiple entries are possible, possible addition of missing residues from disordered regions, or specification of homology or other putative models.
The missing residues were modeled using MODELLER [65].
Both 2QQS and 2GFA structures have missing residues.
In particular, missing residues of the short 24- and 25-residue LRRs of Skp2 are located in the loops.
The 2QQR structure contains the tudor domains with no missing residues.
Each chain is complete and does not have missing residues [51], [68].
Furthermore a reliable homology model for the missing residues is not available.
The missing residues were fixed manually.
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