Protein structure verification

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.

At the WHAT_CHECK pages you will find a more modern and updated explanation of today's WHAT_CHECK features.

WHAT IF I check my structure?

• Introduction
  • Imagine
    • An everyday situation in a biocomputing lab: "Should they use the structure?"
    • An everyday situation in a crystallography lab: "Should they deposit the structure already?"
  • How it all started
  • The need for different kinds of verification tools
  • Where does the knowledge come from?
  • Understanding variations in numbers and standards
  • About "Average" and "Standard Deviation"
  • Z-score?
• A WHAT IF check report: what does it mean?
  • General points
  • Administrative checks
    • Nomenclature
    • Chain name
    • Weights (occupancy)
    • Missing atoms and C-terminal oxygens
  • Symmetry
    • Consistency
    • Cell conventions
    • Matthews' Coefficient
    • Higher symmetry
    • Non crystallographic symmetry
  • Geometry
    • Chirality
    • Bond lengths
    • Bond angles
    • Torsion Angles: "Evaluation"; "Ramachandran"; "omega"; "Chi1/2"
    • Rings and planarity: "Planarity"; "Proline Puckering"
  • Structure
    • Inside/outside profile
    • Bumps
    • Packing quality
    • Backbone: "number of hits"; "backbone normality"; "peptide flips"
    • Sidechain rotamers
    • Water molecules: "floating clusters"; "symmetry relations"
    • B-factors: "average"; "low B-factors"; "B-factor distribution"
    • Hydrogen bonds: "Flip check"; "HIS assignments"; "Unsatisfied"
  • Summary
    • Summary for users of a structure
    • Summary for depositors of a structure