Documentation

Proteins are very simple molecules. They are linear chains of residues. And there are only 20 different residue types.

So far for the theory....

The practice is different:

• We do definitely not understand the mechanism by which protein structures fold. No protein-specific knowledge is used in refinement programs. A large fraction of the refinement procedure consists of an expert looking at the structure, and making manual adjustments.
• Proteins contain thousands of atoms, and it is impossible to keep an overview of everything that is going on by hand.

These two points combined are the origin of "incorrect structures" and "weak points in generally correct structures". The check procedures in WHAT IF were written to help reduce this problem.

WHAT_CHECK has been described in a series of articles that you can find in the article section. WHAT_CHECK is part of the WHAT IF project which you can find here.