Selecting Templates In Swiss Model
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10.9 years ago
Ranjita ▴ 20

I have generated some templates by using template identification option in Swiss Model. Is it possible to select only some of these templates to get the best model? If I select the automated mode, automatically all the templates are getting selected by default.

protein modeling • 5.8k views
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Hi!

Can I extend the the discussion about template selection and automated mode in Swiss-Model?

While I have generated 23 template sequences by clicking on the template identification option, Swiss-Model does not uses all the 23 templates for modeling when I select the automated mode. Instead, only 3 out of the 23 templates are selected by Swiss-Model automatically to do modeling. May I know how does Swiss-Model chooses that 3 templates?

Thanks!!

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10.9 years ago

SWISSMODEL automated mode is suitable only when there is a high coverage and similarity between query and template. SWISSMODEL explains this in their help page.

Selection of a template depends up on various factors: Availability of homologs in PDB, Coverage of query v/s template and Sequence similarity between query and template. A good starting point will be various review articles from Sali Lab.

A typical homology modelling workflow consists of the following steps:

Query sequence -> BLAST PDB -> Retrieve sequence -> Alignment -> Model -> Model validation

In a nut-shell, If you have many templates with good coverage and good similarity score you can select one template and build your model using the alignment. Please ensure that the active site or motifs of interest are within the alignment. For example using the following alignment, if active site residues is in the middle of query protein, you can use either Temp1 or Temp2 as your template. You may also try to generate models using Temp1 and Temp2 and then select the best one after validation and structure analysis.

Query : ----------------------------------------------------- 
Temp1 :   ----------------------------------------- 
Temp2 :   ---------------------------------------------------

If the query doesn't have a single template with a decent coverage, better to select two or more templates.

Query : -----------------------------------------------------
Temp1 : --------------------------------
Temp2 :                            --------------------------

In this case you can use both templates to generate your model.

I have used MODELLER for similar modeling approaches and you can use MODELLER for multiple templates to generate model from multiple templates. The options to use multiple templates is provided in the tutorial. MODELLER also have a web version with limited options. MODWEB. You may also check Bioinformatics Toolkit if you want to access the MODELLER which can accepts custom alignment, so that you can generate model using different models and see the model quality using Ramachandran plot using PDBSum Generate tool.

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Hi Khader Let say I use both template 1 and 2 for modelling by using modeller. For docking its compulsory to study the biology behind the target and template as well. But, it certainly both of template chosen from different information. The things is, after the model has been built using modeller. how can I determined whether the model is built based on template 1 or template 2 for docking study.

Thanks

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