SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: MN: 7. 
Ligands in the template that will be assessed: MN1001, MN1002, MN1003, MN1004, MN1006, MN1007, MN1008. 
Model's ligands section 
MN1001 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.040 
Given the properties calculated previously, the ligand MN1001 will be included in the final model. 
MN1001: conservation:True, RMSD:True, included: True 
 
MN1002 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand MN1002 will not be included in the final model. 
MN1002: conservation:False, RMSD:False, included: False 
 
MN1003 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand MN1003 will not be included in the final model. 
MN1003: conservation:False, RMSD:False, included: False 
 
MN1004 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.050 
Given the properties calculated previously, the ligand MN1004 will be included in the final model. 
MN1004: conservation:True, RMSD:True, included: True 
 
MN1006 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand MN1006 will not be included in the final model. 
MN1006: conservation:False, RMSD:False, included: False 
 
MN1007 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand MN1007 will not be included in the final model. 
MN1007: conservation:False, RMSD:False, included: False 
 
MN1008 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand MN1008 will not be included in the final model. 
MN1008: conservation:False, RMSD:False, included: False 
 
The new model with the included ligands was saved successfully.

Quaternary Structure Annotation of the Template 
 2dho is annotated as MONOMER 
 The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry 
 The following biological unit was used to build the template structure: 2dho.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.104 (>0.5 indicates similarity)

 - Start SMR-Pipeline for:cfcf5df503ac73c43dd17c96c0e817bf on BC2-cluster at Fri Feb 22 16:43:13
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

FATAL - No A3m found

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -      ****************************************************************************
 - building model based on 2dhoA (13-227) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:cfcf5df503ac73c43dd17c96c0e817bf on BC2-cluster at Fri Feb 22 16:44:19
2013