Some other causes of failure may be the presence of non-standard, or modified aminoacids (such as selenomethionine, or phophoaminoacids), alternative conformations, records of anisotropic date, missing backbone atoms (including the absence of a C-terminal oxygen), or backbone atoms with zero B-factors.
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).
The processed PDB entry lists any missing atoms, but does not include them in the coordinate section.
Hydrogen, missing atoms, bonds and charges were computed through Maestro.
To complete the missing atoms, e.g., side-chain atoms or hydrogen atoms, either PyMOL build-residue module or MD simulation software AMBER can be used.
Side-chains with missing atoms are re-constructed using Scrwl 4.0 [9], an important step because energy calculations are highly affected by missing atoms.
Missing side chains (F301, D332, and K5) were re-built, and the missing atoms of K5 were then minimized.
Human-readable annotations on reactions include the reaction definition, equation, a reference to the reaction equation as HTML-image, and the result of the atom balance check (i.e., if there are missing atoms in the reaction).
Entries with missing atoms in the subunit interfaces were discarded.
The missing atoms from the X-ray structures were added using the LEaP module in AmberTools13.
