Structural Assessment

Help

Structural Assessment Introduction

The Model Results page of SWISS-MODEL provides the user with an essential, first glance view of a homology model showing ligands, global and local quality, target-template alignments.

The Structural Assessment page aims to provide more detailed structural information about homology models, with alternative displays and by running additional software tools.

It is also possible to upload your own structures to be structurally assessed.


Structural Assessment Input

SWISS-MODEL homology models can be sent directly to the Structural Assessment page. Open the drop down menu within the model details on the results page of your SWISS-MODEL project.

Upload your own structure in pdb, cif, pdb.gz or cif.gz format. It is also possible to add several structures at a time in a tar or zip archive. If you are logged in, or if you provide an email, the new project will be associated with your account at SWISS-MODEL.

Projects will be deleted automatically from our servers after two weeks.


Ramachandran Plots

A Ramachandran plot is a way to visualize energetically favoured regions for backbone dihedral angles against of amino acid residues in protein structure. Wikipedia

To determine the contours of favoured regions, data was extracted from 12,521 non redundant experimental structures (pairwise sequence identity cutoff 30%, X-ray resolution cutoff 2.5Å) as culled from PISCES. Histograms with a binning of 4 degrees were then used to count Φ (Phi; C-N-CA-C) / Ψ (Psi; N-CA-C-N) occurences for all displayed categories. The number of observed Φ / Ψ pairs determines the contour lines.

General (No Proline or Glycine)
Φ
Ψ
Glycine Only
Φ
Ψ
Proline Only
Φ
Ψ
Pre-Proline Only
Φ
Ψ


MolProbity

MolProbity is a structure-validation web service that provides evaluation of model quality at both the global and local levels for both proteins and nucleic acids.

The SWISS-MODEL Structure Assessment page runs MolProbity within the package Phenix, on the model or structure provided. Full documentation for Phenix can be found here.

The Structure Assessment page hopes to show the most relevant scores provided by Phenix and help the user easily identify where residues of low quality lie in their model or structure. A table of results is presented to the user. For scores-per-residue (or residue-pair), the residues are sorted in decreasing order of quality, so that the lowest quality residue (or residue-pair) is presented first. A tooltip provides the score for the residue/pair.

ScoreCommentIdeal Case
MolProbity ScoreCombined protein quality score that reflects the crystallographic resolution at which such a quality would be expectedAs low as possible
Clash ScoreClashes show > 0.45Å non-H-bondZero
Ramachandran Favoured> 98%
Ramachandran OutliersAt resolutions below 3.0Å, any outliers should be considered errors.< 0.2%
Rotamer OutliersAt resolutions below 3.0Å, any outliers should be considered errors.< 1%
C-Beta DeviationsPosition deviates from ideal by > 0.25ÅZero
Bad Bonds> 4σ deviations from idealZero
Bad Angles> 4σ deviations from idealZero
Cis/Twisted Prolines/Non-Prolines< 30° from ideal defined as CIS; >150° from ideal defined as TwistedZero

Before MolProbity is run, it should be noted that the following steps are performed on the users uploaded structure.

Uploaded Structure
If mmCIF, converted to PDB, first biounit is selected
Chains with < 15 residues are discarded
MolProbity


Quality Estimate

QMEAN (Benkert et al.) is a composite estimator based on different geometrical properties and provides both global (i.e. for the entire structure) and local (i.e. per residue) absolute quality estimates on the basis of one single model. Please read the SWISS-MODEL help and for full details, please refer to the publication.

For SWISS-MODEL Homology models, QMEAN will have been calculated during the normal modelling pipeline process. For uploaded structures, QMEAN will be started as a separate job using the QMEANDisCo method.


Residue Quality

The residues found in all protein polypeptide chains of the model are displayed in an interactive sequence display. Each residue is displayed by its one letter code below a bar chart displaying the QMEAN local quality estimation value.

The secondary structure of the protein, either DSSP or PSIPRED, is displayed above each residue code as a single letter. DSSP is calculated using the DSSP implementation in OpenStructure.

To change representation between DSSP and PSIPred, click the icon to the top left of the sequence. Setting the choice of secondary structure will also update the structure in the 3D Viewer.