SWISS-MODEL WORKSPACE TUTORIAL

How can I assess geomoetrical accuracy of a structure or model?

Evaluation of model quality is a crucial step in homology modeling. While the performance of the automated SWISS-MODEL (Schwede et al.) pipeline in general is continuously evaluated by the EVA project (Koh et al.), the quality of individual models can vary significantly.

Therefore, graphical plots of Anolea mean force potential (Melo et al.), GROMOS empirical force field energy (van Gunsteren et al.), Verify3D profile evaluation (Eisenberg et al.), Whatcheck (Hooft et al.) and Procheck (Laskowski et al.) reports are provided to enable the user to estimate the quality of protein models and template structures.

Procheck

The PROCHECK suite of programs (Laskowski et al.) assess the "stereochemical quality" of a given protein structure. The aim of PROCHECK is to assess how normal, or conversely how unusual, the geometry of the residues in a given protein structure is, as compared with stereochemical parameters derived from well-refined, high-resolution structures.

What Check

What Check comprises several tools for protein structure verification (Hooft et al.). Besides of a detailed report, a summary for "users of a structure" is provided. Detailled documentation for the WHAT_CHECK output is available at the WHAT_CHECK homepage.

Example outputs: