PRIMO-COMPLEXES
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      Status: Queued
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PRIMO-COMPLEXES (PRotein Interactive MOdeling)

PRIMO-COMPLEXES is an interactive homology modeling pipeline.


Required input
The key can be obtained from the Modeller website

analysing sequence ...
Upload Sequence file:Choose Sample Sequence :
Build biological assembly?

Optional input



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Off

Automatically identify templates
Manually specify which of the identified templates to use during modeling?
HHSuite database version: Sat Aug 28 15:48:47 SAST 2021 BLAST database up-to-date as of Wed Aug 4 15:18:56 SAST 2021


Manually edit generated alignment?

T-COFFEE
MAFFT
MUSCLE
CLUSTAL-O


The prefix to use when naming models

Start

Copyright © RUBi all rights reserved.
Margaret Nabatanzi, and Özlem Tastan Bishop


Funders

  • National Institutes of Health Common Fund (grant number U41HG006941)
  • National Research Foundation (NRF), South Africa, (grant number 93690)
  • Rhodes University, Research Office, Postdoctoral Fellowship

Cite Us


  • Hatherley R, Brown DK, Glenister M, Tastan Bishop Ö. “PRIMO: An Interactive Homology Modeling Pipeline.”  PLoS One.  2016 Nov 17;11(11):e0166698. doi: 10.1371/journal.pone.0166698.




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Job History

Select a job:

  • Status: Created
    Status: Queued
    Status: Running
    Status: Awaiting User Input
    Status: Completed Successfully
    Status: Awaiting User Input
    Status: Completed Successfully
    Status: Failed
    Status: Stopped

New Job

Step 1
Template Identification
Step 2
Target-Template Alignment
Step 3
Modeling
Step 4
Building Full Complex
Step 1
Template Identification
Step 2
Target-Template Alignment
Step 3
Modeling

Job Summary:

Created Queued Running Awaiting User Input Completed Successfully Failed Stopped
1
Template Identification
Created Queued Running Awaiting User Input Completed Successfully Failed Stopped
Specified templates
Uploaded templates
2
Target-Template Alignment
Created Queued Created Running Awaiting User Input Completed Successfully Failed Stopped
Standard Pspresso
Standard Pseudo-Homologs
3
Modeling
Created Queued Created Running Completed Successfully Failed Stopped
Very slow Slow Fast Very fast None

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

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:
  • Edit & Continue
Last DB update:
Template A.U chain Identity (%) Coverage Resolution Biounit oligo state Description Determined by Options Selected? More
Show Hide
  • Select ligand
  • Select ligand
Other Biological Assembly(ies) Biounit oligo state Determined by Options Selected
Show Hide
  • 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

This step failed to execute successfully. Please check your input and try again.

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 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
  • Edit & 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:
Export Alignment (Fasta)
Invalid Alignment
X
Missing residue
.
Modified residue
-
Gap

This step failed to execute successfully. Please check your input and try again.

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

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

Continue Continue
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 Select All Deselect All
n/a
Show Hide
  • Structure Evaluation
Back
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)

This step failed to execute successfully. Please check your input and try again.

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

Producing 1 full protein complex using PyMOL

The full protein complex has been built successfully using PyMOL.
The model along with the template used are listed below:
Download Selected
Name RMSD Options Select All Deselect All
n/a
Show Hide

This step failed to execute successfully. Please check your input and try again.

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

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The next step has been run before. Running it again will create a new job, which will continue on from the currently selected step i.e. .

Manually edit generated alignment?

MAFFT
MUSCLE
T-COFFEE
CLUSTAL-O
No. of models to generate:
Refinement method:

Job options

Select identification method

HHSuite database version: Sat Aug 28 15:48:47 SAST 2021 BLAST database up-to-date as of Wed Aug 4 15:18:56 SAST 2021

You may edit the future stages once templates are identified

Select Ligands

Name Chain Residue No. Selected?

Choose Sample Sequence

Protein Complex Protein Monomer
>target_0 VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDN LKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
>target_1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNAL SALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
>target_0 ATKAVAVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEEEDNTAGCTSAGPHFNPLSRKHGGPKDEERH VGDLGNVTADKDGVADVSIEDSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGKIGKAQ

PV-MSA Structure Viewer