A QUICK GUIDE TO ANALYSE SWISS MODEL RESULTS

Look for theoretical models at SWISS-MODEL Repository

(Automatically generated protein models database) or

• Use First Approach mode

In the first case, you will receive TraceLog and Whatcheck if you will send again the PDB file as a new project.

TraceLog file

Contains information about modelling processes.

• Inspect identities of the template(s) to the problem sequence, and the corresponding alignment:

         12UCE.pdb: 22.85 % identity
         11AYZ.pdb: 27.8 % identity
         11AAK.pdb: 17.15 % identity
         12AAK.pdb: 17.15 % identity
         11UCZ.pdb: 29.6 % identity
         12UCZ.pdb: 29.6 % identity
         11A3S.pdb: 22.5 % identity

         Looking for template groups
         Global alignment overview:

         Taget Sequence: |====================================================================|
         12UCE.pdb       |                  -------------------------------------------------
         11AYZ.pdb       |                    ------------------------------------------------
         11AAK.pdb       |               -----------------------------------------------------
         12AAK.pdb       |               -----------------------------------------------------
         11UCZ.pdb       |                 --------------------------
         12UCZ.pdb       |                 --------------------------
         11A3S.pdb       |                 --------------------------------------------------

         AlignMaster found 1 regions to model separately:
                 1: Using template(s)   11A3S.pdb 11AAK.pdb 11AYZ.pdb 11UCZ.pdb 12AAK.pdb 12UCE.pdb 12UCZ.pdb

         12UCE.pdb has been rejected,  too low similarity with Target sequence (22.85 % identity.)
         11AAK.pdb has been rejected,  too low similarity with Target sequence (17.15 % identity.)
         12AAK.pdb has been rejected,  too low similarity with Target sequence (17.15 % identity.)
         11A3S.pdb has been rejected,  too low similarity with Target sequence (22.5 % identity.)
 
 

• Inspect the loop building part:

PDB file

Contains the alignment and the coordinates of the model and template(s).
 
• Inspect the alignment. Secondary structure prediction of the TARGET must be similar to the corresponding secondary structure of template(s):

• View the file (using Rasmol: backbone, coloured by temperature).

In blue, fine energies; in red, bad ones (normally common for loops):
 

Whatcheck file

Contains information about the quality of the model.
 
• Inspect the part named Summary report for users of a structure:

 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.842
  Bond angles                    :   1.273
  Omega angle restraints         :   1.125
  Side chain planarity           :   2.571 (loose)
  Improper dihedral distribution :   1.768 (loose)
  B-factor distribution          :   3.632 (loose)
  Inside/Outside distribution    :   1.073
 

and compare with the template(s) PDBREPORT (protein verification by WHAT_CHECK procedures)
-for example, for 1AYZ-:

Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.273
  2nd generation packing quality :   0.005
  Ramachandran plot appearance   :  -1.147
  chi-1/chi-2 rotamer normality  :  -0.625
  Backbone conformation          :   0.430
 

RMS Z-scores, should be close to 1.0:

  Bond lengths                   :   0.335 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   0.229 (tight)
  Side chain planarity           :   0.539 (tight)
  Improper dihedral distribution :   0.629
  Inside/Outside distribution    :   0.973
 

• Compare also the rest of the file, mainly, at a first sight, for the part named

Buried unsatisfied hydrogen bond donors and acceptors:
 
Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.