Hi Priyadarshini,

Go through this paper, it gives good information regarding Ag-Ab modeling, docking, validation, interaction study.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039950/

See If you get access to Schrodinger software you can use PIPER. Here is the link. But yes its paid(very costly). But the result obtained at the end is very good as it has Docking/Analyzing option for Antigen-Antibody.

http://www.schrodinger.com/PIPER/

May be you can go forth with docking and MD using existing IgG structures. But, the problem is the CDRs. Those are the most variable and most important regions of the immunoglobulins. The highly antigen specific hypervariable regions are modelled by lymphocytes by a process called affinity maturation (somatic hypermutation/V(D)J recombination followed by clonal selection). Modelling specific CDRs in silico is a challenging task.

Thank you Mr. Uttam. Docking with Ig G molecule with exact CDR is the step where I am stumbling upon to validate the modelled protein to be antigenic. Antigenic epitopes have been predicted using online servers (EMBOSS, VaxiJen). and I am not sure whether in vitro testing is feasible for validation, by synthesising this antigen and reacting it with patient serum. Anyhow, to my knowledge, that is time consuming. Hence I m searching for in silico methods to validate the antigenic protein,

How in general will antigen antibody interactions be carried out by in silico methods?

For my study, hope I should proceed with in vitro methods only.

Hi Priyadarshini,

Go through this paper, it gives good information regarding Ag-Ab modeling, docking, validation, interaction study.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039950/

See If you get access to Schrodinger software you can use PIPER. Here is the link. But yes its paid(very costly). But the result obtained at the end is very good as it has Docking/Analyzing option for Antigen-Antibody.

http://www.schrodinger.com/PIPER/

Dear Piriyatharisini, suggestions I can give based on the experiences I made so far on docking are:

- As Ag-binding loops are rather "flexible" it may be a good idea to incorporate backbone flexibility into your docking process - there are a number of ways this can be done, and the best option might be a combination of those:

- the docking program I can recommend is HADDOCK (current version 2.2). It investigates different degrees of flexibility (from side-chain flexibility to whole-complex MD in explicit solvent) during docking and is especially recommendable if there is experimental information about the complex available (for example mutagenesis data or bioinformatic predictions, however it is also possible to perform "global docking" or limit the search to certain parts of the proteins, like the CDRs). HADDOCK is free for academic use and there is also a webserver available: http://haddock.science.uu.nl/

- since the movement of the loops during docking is nevertheless limited, you could try to perform MD simulations of the variable domains of your Ab and try to dock for example the most visited clusters of loop conformations to NMR ensembles of your Ag, if available.

Also, an in silico model is a model and not necessarily the "truth" but it can help to direct further investigations.

Best regards,

Jan

http://haddock.science.uu.nl/

Thank you so much Mr. Sanket Bapat. I have gone through the paper which you have sent, it was really useful and informative.

Thank you very much for your valuable suggestions Mr. Jan Walther. I ll try out the HADDOCK program for my work.

For the basic idea, I would recommend to try Zdock. User friendly protein-protein docking. (http://zdock.umassmed.edu/) Generally, this program is embeded in DS program which further analyse by Rdock.