PRIMO - PRotein Interactive MOdeling

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Step 1

Template Identification

Step 2

Target-Template Alignment

Step 3

Modeling

Job Summary:

Status:

Created Queued Running Awaiting User Input Completed Successfully Failed Stopped

Submitted At:

Finished At:

Target sequence:

Template Identification

Status:

Created Queued Running Awaiting User Input Completed Successfully Failed Stopped

Submitted At:

Finished At:

Identification method:

Specified templates

Identification method:

Uploaded templates

Target-Template Alignment

Status:

Created Queued Created Running Awaiting User Input Completed Successfully Failed Stopped

Submitted At:

Finished At:

Alignment program:

T-Coffee mode:

Standard Pspresso

MAFFT mode:

Standard Pseudo-Homologs

Modeling

Status:

Created Queued Created Running Completed Successfully Failed Stopped

Submitted At:

Finished At:

No. of models:

Refinement method:

Very slow Slow Fast Very fast None

Waiting to start...

This stage is not yet running. This is most likely, because it is waiting for a previous stage to finish.

Searching for suitable templates...

Querying HHSearch BLAST with your target sequence. Depending on the length of your sequence, this may take up to 15 minutes.

Template identification: Tips and tricks

Always check the quality of the templates you choose for modeling
- You can examine the structural validation for each template on the PDB website
- Clicking on the PDB ID in the results table will take you to its entry in the PDB

The following structures were identified as suitable templates using HHSearch using BLAST . Select one or more to continue:

Last DB update:

Template	Chain	Identity (%)	Coverage	Resolution	Options	Selected?
						Show Hide Select ligand Select ligand

Note: selecting a ligand in the visualizer below does not select it for modeling. See 'Options' dropdown in the templates table for ligand modeling.

Select Coverage

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This step was cancelled before it could finish executing. This may be, because a previous stage failed to execute or, because of user intervention.

Aligning sequences...

Aligning using HHSearch. in standard mode. in 3D-COFFEE mode. in standard mode. in Pseudo-Homologs mode. This process should be completed within a minute or two.

Sequence alignment: Tips and tricks

If there are large gaps in your alignment, try using an additional template that covers this region of your protein
Try using different alignment programs

Continue Continue

The following alignment was generated using HHSearch in standard mode in 3D-COFFEE mode in standard mode in Pseudo-Homologs mode (edited by user): The following alignment was uploaded:

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Missing residue

Modified residue

Gap

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This step was cancelled before it could finish executing. This may be, because a previous stage failed to execute or, because of user intervention.

Generating models...

Producing models using Modeller9v15 with very slow slow fast very fast no refinement.

Modeling: Tips and tricks

When assessing models, try using different Model Quality Assessment Programs (MQAP)
Examples of MQAPs:
- ProSA (local + global)
- QMEAN server (local + global)
- Verify 3D (local + global)
Use local evaluation methods to find problem areas in your models and focus on improving these areas

The target sequence was modeled successfully using very slow slow fast very fast no refinement. The models along with the templates used are listed below:

Download Selected

Name

Dope Z-Score

RMSD

Options

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n/a

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See below for reports on structure/model quality. Additional structure evaluation servers can be accessed at the following links:

ProSA (local + global)
QMEAN server (local + global)
Verify 3D (local + global)

Evaluation method:

Report:

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This step was cancelled before it could finish executing. This may be, because a previous stage failed to execute or, because of user intervention.