Questions and Answers

Do you have a question? Contact us!

1 ) How do I start homology modeling? Do I need to log in?

In order to start homology modeling click on the 'Model a GPCR' button -- no registration is necessary. Nonetheless a registration option is provided if you want to keep track of your projects under an account name.

2 ) Why is nothing happening when I click on 'help' or some other hyperlinks?

It's probable that javascript has been disabled in your browser. Make sure that you enable javascript in your browser settings.

3 ) Why is the N-terminal modeled if one selects TM1? (C-terminal if one selects H8?)

The default implementation is to consider the region TM1 as the segment that expands from N-ter until the beginning of IL1; accordingly, the region TM8 goes from the end of TM7 until the C-ter. If you want to exclude the disordered N-ter or C-ter regions, for which no template is probably available, you should simply delete the corresponding sequence region from your query sequence.

4 ) Why can't I model sequences longer than 600 residues?

The reason is two-fold. In the one hand, GPCR sequences larger than 600 amino acids will be that long due to large N-terminal or C-terminal tails which are not present in the crystal structures. And in the other hand our MD-equilibration protocol for GPCR's larger than 600 residues would require a computational time longer than the 24 hour cutoff we can offer at the moment.

5 ) My favorite browser is Konqueror or one of these.

Primarily we test on Safari, Chrome, IE, Firefox... Please consider using one of the tested browsers.

6 ) Why can't I edit a sequence alignment online, as suggested by the tutorial?

The reason is that we are using JalView to edit sequences online and it depends on having a browser that allows Java plugins such as Firefox. If you're using chrome you can download the alignment and edit it using SeaView, or AliView, or ClustalX, or other popular standalone alignment editors and then upload your edited alignment.

7 ) How do you align target sequences against a selected profile?

We use clustalW2 to perform a sequence to profile MSA.

8 ) I get a highly unstructured model for a loop region. Why is this and how can I solve it?

You are facing an inherent problem faced when modeling loop regions: the lack of a template structure. The current implementation of GPCR-ModSim models the loop regions based on the homology with the template sequence(s), if that exists at all. Thereafter LoopModel is also offered as a routine to refine loop regions, where no template is needed. However, this method is know to have a limitation of sequence length of about 10-12 residues, and beyond that sequence length the models will be unreliable. What we recommend is that you 'engineer' your sequence, i.e. create a chain break in your sequence and do not attempt to model longer loops, in the same way that some of these loops are not observed in crystal structures, or the crystal structures have even been engineered to have deletions or fusions with stabilyzing proteins in these unstructured regions. More advanced loop modeling routines are a matter of research in the modeling community and we plan to implement alternative methods in the future in GPCR-ModSim, keep posted.

9 ) I try to create a project and I get the message 'This project already exists'.

You have used the same project name in the same session. You should use a different project name or restart your browser, then the projects that you created will be automatically removed. NOTE however that if you have created a login, you will have access to your projects for several weeks, but then you cannot repeat project names because this will create a conflict with the database.

10 ) How do I know the list of templates that GPCR-ModSim is offering?

The currently available templates are available on the following links: Active, Active-like, Inactive.The crystallization of GPCRs is in a golden era, and we are very pleased with this. But this is requiring for us to constantly update our list of templates and curate our master sequence alignment (MSA) on each cathegory. If you do not find one of the latest crystal structures in your template list, please be patience, we will include it very soon!