PRIMO (PRotein Interactive MOdeling)
PRIMO is an interactive homology modeling pipeline.Cite Us
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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 Summary:
Template Identification
Target-Template Alignment
Modeling
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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
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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
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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
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Producing models using Modeller9v15 with very slow slow fast very fast no refinement.
Modeling: Tips and tricks
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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
- ProSA (local + global)
- QMEAN server (local + global)
- Verify 3D (local + global)
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