GPCRM web service

A web service to predict structures of G-protein-coupled receptors (GPCRs) using advanced homology modeling tools: profile-profile alignment, multiple structural templates, and Z coordinate-based filtering of resulting models. Two distinct loop modeling techniques are employed - Modeller and Rosetta - and the proper scoring is used to score the final ranking list of GPCR models.

Filling the input data entry.

The selection of templates is based on sequence similarity between query and templates calculated using multiple sequence alignment of a query sequence and all GPCRs sequences whose 3D structures are available in PDB. In the current version of the service we used a set of templates structures presented in the Templates section . If you mark the lysozyme option, then during modeling a set of templates is narrowed to those which has lysozyme version.

Here type your name or nickname (maximum number of characters: 100). It is obligatory.

We suggest to type your academic address here. It is obligatory.

Here type the name of your temporary task for convenient identification of your results. For example, let's type 'CB2 cannabinoid receptor - inactive' since this is the receptor we are going to model.

Allowed format: fasta or plain sequence. To obtain the sequence of CB2 cannabinoid receptor go to http://www.uniprot.org/ and search for 'CB2'. Then click on P34972 at the very left of 'CNR2_Human' entry, scroll down until you find a sequence and click 'FASTA' button. Either copy-paste the CB2 receptor sequence in the box provided, or save FASTA sequence file to disc and then click "Choose File" button below to upload the sequence file.

To improve accuracy of the alignment and model building provide the suggested disulfide bridge between the extracellular loop 2 and the trans-membrane helix TM3. In our example (CB2) the disulfide bridge is not located between the EC2 and TM3 so those fields will be left empty.

# To improve accuracy of the alignment and model building provide the suggested disulfide bridge between the extracellular loop 2 and the trans-membrane helix TM3. # For example in CB2 receptor the disulfide bridge exists between C174 and C179, so we type '174' and '179' in 'Cys 1:' and 'Cys 2:' fields accordingly. # Those fields can be left empty as well. #

Choosing the right options.

Task Mode: Auto - all steps of the modeling procedure are processed without any User's intervention.
Advanced - a User can change: subset of templates used in the modeling (first step) and the query-templates alignment and loops which are remodeled (second step). Since this tutorial is for beginners we choose Task Mode: Auto

Set of Templates: We provide 2 subsets of templates: PDB structures bound to agonists (named: active ) and PDB structures bound to inverse agonists or antagonists (named: inactive). For the purpose of this tutorial we want an inactive CB2 receptor model, so in this field we choose 'Inactive'.

Models mode: Long path - loops are extensively sampled by Rosetta (thousands of loops built, long computation time),
Quick path - fewer loops are generated by Rosetta which allows to shorten the computation time while keeping quality of results on average,
High Similarity - generation of novel loops by Rosetta is omitted. The loops are taken from templates or generated by Modeller if missing.
Here, we can select High similarity (in this case all loops are taken from CB1 template) - results 1 hour, or
Quick path (loops between TMH are modeled de novo by Rosetta) - results in about couple of hours.

Lysozyme: This option was left for historical reasons only and will not be discussed here. For this tutorial leave the default setting of this parameter 'Do not add from template'.

GPCRM uses the Modeller software which requires prior free registration at http://salilab.org/modeller/registration.html.

Rosetta loop modeling: This option was left for historical reasons only and will not be discussed here. For this tutorial leave the default setting.

Now, the all fields of input data are filled and settings for AUTO task mode are chosen, so it is possibility to launch the 'Run Query' button and it is necessary to wait for results. Good Luck!

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