I cannot see the molecular models.
When do you update the database?
Why is my mutation not (yet) in GRIS?
What's up with the residue numbering schemes?
Which molecular viewer do you recommend?
Can I make screenshots or nice pictures of the models?
What exactly is "the correlated mutation finder" I see in the visualization section?
How did you make the models? Are they reliable?
What is a flat text file and how do I read this?
Jmol: Can I calculate and visualize the distance between atoms?
Jmol: Can I visualize a residue without going back to the selection list?
I cannot see the molecular models.
Make sure you have Java installed. Java is a common and widely used browser plug-in.
Click here to download and install Java now.
When do you update the database?
GRIS updates are scheduled every month, depending on the availability of new mutation data in the literature.
Why is my mutation not (yet) in GRIS?
There could be two reasons.
First, a significant amount of the mutations comes from the GPCRDB. Florence Horn from the GPCRDB has made a program called MuteXt
to search for mutations in the literature. Automation is never perfect, so that's the reason why some mutants are not found.
Second, only mutations that have been published in the literature will appear in the database. Moreover, the paper has to be
officially published, so accelerated publications will not be considered. This may indeed cause a delay, but just be patient.
If your mutation however does meet these requirements and it is not in GRIS, feel free to drop me (JVD) a mail and we'll get it fixed.
What's up with the residue numbering schemes?
For the ectodomain, we have created a general numbering scheme to facilitate searching through the database, visualizing residues and
communication between scientists in the field. Whenever one talks about residue 5050 of the ECD, we now all know this is the X3
residue between two hydrophobic residues in LRR5. See the numbering section for more info.
For the transmembrane part, two numbering schemes are used today. Very unfortunate, since this complicates communication between
scientists and it definately complicates the database management. ;-)
Both schemes are implemented in GRIS. See the numbering section for more info.
Which molecular viewer do you recommend?
First of all, all models you can view on this website are presented with the Jmol java application. This is very handy for
websites, but less straightforward to use as a stand-alone viewer.
I recommend getting the free YASARA View program from http://www.yasara.org.
It works in Windows as well as in Linux and Mac. You will have to register, but it takes only a few seconds. And it's worth it.
Can I make screenshots or nice pictures of the models?
Sure you can. You can choose to do a "Print screen" from the Jmol pages on this website, but for high-quality images, I recommend
YASARA View again. When you already have YASARA View, you need to download PovRay from http://www.povray.org.
Then you have to tell YASARA to use PovRay as an image renderer. The instructions are in the YASARA documentation (on your computer) in "yasara/doc/Gs.html".
GRIS also offers a tool to create high-quality molecular images online using the YASARA graphics engine. Click here to start creating your personalized image.
What exactly is "the correlated mutation finder" I see in the visualization section?
You will only see this link when you view a model of the transmembrane part of a receptor.
An example. Let's say you are interested in residue 5.54 from TM5 in the TSHR. But at the same time you see that this residue
is another aminoacid in the FSHR and LHR. Wouldn't it be nice to know whether aminoacids close to 5.54 also change when 5.54 changes?
Then you might find a real and maybe functional interaction between residues.
This is what the Correlated Mutation Finder tries to tell you. You have two positions in your mind that could show correlated mutation
behaviour, you feed them to the program (you can also narrow your search to only search in specific families), and what you
get is a list of these residues at those positions.
When you see that these two residues mutate "in tandem" (when one changes, the other changes), then you might have found a putative
interaction in the receptor.
This is of course a very simple way of finding such interactions. To do more extensive Correlated Mutation Analysis (CMA), I recommend
using the WHAT IF software.
How did you make the models? Are they reliable?
All models were initially built with the WHAT IF modeling software using a position-specific backbone rotamer library.
For the modeling of the ectodomain, the structure of the human FSHR (PDB: 1XWD) was used as a template.
For completeness, also the bound hormone was modelled (if the sequence was available). So, the model of the human TSHR includes human TSH, the model of the rat FSHR includes rat FSH, etc ...
The models of the transmembrane portion were build using the bovine rhodopsin structure (PDB: 1GZM) as template.
The alignment used can be found HERE.
'Raw models not energy minimized' come directly from the WHAT IF software without any modification. We suggest you use these models if you want to
do energy minimization or molecular dynamics yourself for further analysis.
'Models energy minimized with YASARA' were also generated with WHAT IF, but to remove bumps and correct the covalent geometry, the structure was
energy-minimized with YASARA by applying the Yamber2 force field, using a 7.86 Å force cutoff. After removal of conformational stress by a short steepest descent minimization,
the procedure continued by simulated annealing (time step 2 fs, atom velocities scaled down by 0.9 every 10th step) until convergence was reached, i.e. no energy improvement was found for 200 steps.
Disclaimer: the models were built completely automatic, without manual changes afterwards. Use them at your own risk. We cannot be held responsible for
errors in the models.
What is a flat text file and how do I read this?
All mutant information can be obtained as a flat text file. The link to the text file is on the mutant details page.
A flat text file has the advantage of being human and machine readable.
Every flat text file of a mutant you find in GRIS is formatted in the same way, allowing for easy processing by programmers who want to make further use of the mutant data available in GRIS.
Fields in a flat file in GRIS are separated by a tab character.
The order of the fields is the following (a slash (/) is used here instead of tab to separate the fields):
Mutation / Accession code / Receptor / Species / Ballesteros (TM) or GPMD (ECD) number / GPCRDB number / Number in the PDB files available from GRIS / Domain / Subdomain / Constitutivity (Y=Yes, N=No, NA=Unknown) / Expression level (% of WT, NA=Unknown) / Binding affinity (U=Unchanged, I=Increased, D=Decreased, NA=Unknown) / Additional comments / PubMed number(s) (separated by a hyphen (-) when more than one) / Original full length sequence / Aligned sequence
Jmol: Can I calculate and visualize the distance between atoms?
Yes you can. Make sure you visualize the atoms first. Double-click on the first atom, the mouse pointer will become a cross now.
Then point your mouse on the second atom and Jmol tells you the distance. Double-click on the second atom to draw a line between the
atoms indicating the distance.
Jmol: Can I visualize a residue without going back to the selection list?
Yes you can. Click on the residue (or just on the backbone) you would like to show up. At the bottom of your browser (the status bar), you will see the
properties of the residue you just clicked. Something like "VAL[79]:A.CA #611". The number after the three-letter aminoacid code
is the residue number in the PDB file (not the general number or swissprot number!) and this is what you need.
Now type in the "Custom Jmol script"-box the following: select 79; wireframe on;
For more information on the Jmol script language, please visit the Jmol homepage or Bob Hansons interactive scripting documentation