Hi Robert,

You can start by reading about Class A GPCRs. ( http://en.wikipedia.org/wiki/Rhodopsin-like_receptors )

If you are going for ligand screening, you must go for finding the binding pocket first.

There are few softwares available which will work for you to find binding pocket. Look into the below mentioned link for the softwares have suffices Pocket.

http://proline.physics.iisc.ernet.in/home/Software_and_Databases#Mtb_Structurual_Annotation_Database

You may use them to identify the pocket. Once you have identified the pocket you can start analyzing these pockets and finding suitable ligands.

A smarter way to start with would be just do the sequence alignment of your given protein sequence which in your case its Rhodopsin like receptor which is one of the highly explored class of GPCRs with crystal structures available for them. Then find the best homology model and search for the associated ligands to it and from there you can start building your own ligand analogs for finding the potentl inhibitors.

Then the simple procedure after that would be designing ligands and using ligand-protein docking techniques to screen potential inhibitors based on various parameters such as Binding free energy, probability of binding, inhibitory constant etc.

Note: The above mentioned softwares are build on very large data sets which enhances the accuracy of predicted model. However, in case of any difficulty one must use his logical reasoning to deal with it.

I hope this helps.

Best wishes

http://proline.physics.iisc.ernet.in/home/Software_and_Databases#Mtb_Structurual_Annotation_Database

You can start looking into the active site of the receptor. There are several online tools available to pridict the active site. Once you find out the active sites for your receptor, perform docking studies. The ligand which will fit in the binding site with least energy value can be the potential ligand.

Hello Robert.

                       Due to too much pressures in my studies lately, I could not reach your question until today. See below my suggestions.

For class Q GPCR , search PBD database using your protein sequence at hand.

This database contains some of the class A GPCR that have been co-crystallized with native ligands into the active site of the protein. 

If you worries is in indicating the precise binding pocket of the protein, then download all crystallize GPCR 3d structures, in PDB and run sequence alingment, for your protein. Compared the active sites of the PDB proteins, where the native ligands were attached to that of yours. I mean you should try to idientify common residues in the binding pocket and then confirm that it is the binding pocket of your protein, if more than 40% of the residues match.

NB: If you donot have 3D crystal structure of the target GPCR at hand, then you might  want to go further by doing homology modeling. It might be difficult for you to do homology modelling using softwares at hand, so i recommend you do it online using: swissmodel.expasy.org . It is pretty simple to do it. all you need is submit the task and get back results.

If you have 3D structure or you have done the Homology modeling:

Now remove all native ligands from the binding pocket of the PDB porteins and then dock it into the binding pocket of your own protein.

If these ligand perform well, i mean check all binding poses with your protein and compare the binding poses of the native ligands with that of the PDB proteins and their native ligands.

Then design a ligand to fit well by looking at the constraints of the binding pockets. This procedure is very tedious and requires alot of extensive checking and Molecular dynamic simulations to base conclusion on suitable binding poses.

Now if you confirm the structure of the desired native ligands, then you have to use this ligand and then search the chemical databases for similar ligands to dock into you protein, or visit the chemistry department (Computer lab) and request assistance with 3D structure activity relationships of the native ligands. They will help you very much.

If you are unable to do this, then you might want to consider extending me a visit during the summer holidays in hasselt. 

I will find time to answer the other questions.

Thanks for your time and good luck.