How to use the GPCRDB

• Using the available help

  The first thing you need to know is how to use the help system. The database contains a lot of help information, helping you getting the most out of this resource. The help is 'context-sensitive', meaning that it is there where you need it (and not in your way when you don't). Wherever help is available, this icon:

  It works!

  appears. Clicking it will open a popup window containing the help (try it!).

Locating data

• Finding proteins

  You can search for proteins by navigating to the search page and specifying your search criteria there. To get to the search page, click the 'Search' link in the navigation menu at the top of the page. The search page can be used to search for a number of different things, but the default search type is proteins. Once you are at the search page, clicking the help button will explain all to you about what the options in the search form mean and how to use them.

• Finding alignments of a protein family

  The first step in finding the alignment of a protein family is locating the family. The easiest way to do that is by using the search page. To get to the search page, click the 'Search' link in the navigation menu at the top of the page. The search page loads the protein search panel by default but clicking on the 'Family search' tab takes you to the the form where you can search for your protein family. The help on that page will tell you more about how to use the search form. Once you have found you protein family you can navigate to the alignment by clicking the 'open alignment' link.

• Finding mutations

  You can search for mutations by navigating to the search page and specifying your search criteria there. To get to the search page, click the 'Search' link in the navigation menu at the top of the page. The search page loads the protein search panel by default but clicking on the 'Mutant search' tab takes you to the the form where you can search for mutations. Once you are at the search page, clicking the help button will explain all to you about what the options in the search form mean and how to use them.

• Finding ligand binding data

  Currently there is no search option specific for ligand binding data. You can however find ligand binding data for a protein of interest by navigating to the page with detailed information about that protein. Look at the 'Finding proteins' item to learn how to find your protein. If you select the 'has ligand binding data' option in the protein search field, you make sure that you only find proteins for which there is ligand binding data available. Once you are at the page with details about you protein, read the help in the 'Ligand binding data' section there about how to interact with this data.

Using services & tools

• BLAST

  You can find proteins in the database that have a sequence similar to your sequence by using the BLAST functionality. Navigate to the BLAST tool by hovering your mouse over the 'Tools' menu item at the top of the page and clicking the 'Blast' link. Extensive help about how to use this tool is available there.

• Creating your own alignments

  You can create your own alignments by using the alignment builder. To get there, hover your mouse over the 'Tools' menu item at the top of the page and click the 'AlignmentBuilder' link. Extensive help about how to use this tool is available there.

• Predict the effect of a mutant

  To predict the effect of a (class A) mutant you can use the mutation predictor tool. To get there, hover your mouse over the 'Tools' menu item at the top of the page and click the 'MutationPredictor' link. Extensive help about how to use this tool is available there.

• Analyzing alignments

  There is a very extensive alignment analysis page available for all GPCR families. You can investigate things like entropy and variability using interactive plots and 3D visualizations. These pages are available from the protein family pages. Click on any protein in the protein family page, then click the link 'Alignments and Analysis', and from there navigate to the 'Analyze' page.

• Using webservices

  To use the services offered by the GPCRDB, you will need the WSDL (available under "Tools - WebServices") to generate your own client. More detailed information about how to do this will be made available.