SWISS-MODEL WORKSPACE TUTORIAL

How can I assess a structure or model with empirical force-field and Mean Force Potential methods?

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.) and Verify3D profile evaluation (Eisenberg et al.) are provided to enable the user to estimate the quality of protein models and template structures.

Anolea: The atomic empirical mean force potential ANOLEA (Melo et al.) is used to assess packing quality of the models. The program performs energy calculations on a protein chain, evaluating the "Non- Local Environment" (NLE) of each heavy atom in the molecule. The y-axis of the plot represents the energy for each amino acid of the protein chain. Negative energy values (in green) represent favourable energy environment whereas positive values (in red) unfavourable energy environment for a given amino acid.

Verify3D: The Verify3D (Eisenberg et al.) method assess protein structures using three-dimensional profiles. This program analyzes the compatibilty of an atomic model (3D) with its own amino acid sequence (1D). Each residue is assigned a structural class based on its location and environment (alpha, beta, loop, polar, apolar etc). Then a database generated from good structures is used to obtain a score for each of the 20 amino acids in this structural class. The vertical axis in the plot represents the average 3D-1D profile score for each residues in a 21-residue sliding window. The scores ranges from -1 (bad score) to +1 (good score).

Gromos: The y-axis of the plot represents the GROMOS (van Gunsteren et al.) empirical force field energy for each amino acid of the protein chain. Negative energy values (in green) represent favourable energy environment whereas positive values (in red) unfavourable energy environment for a given amino acid.