Custom antibody-antigen affinity prediction

[zkhan]

Hi, I am a research student currently in high school. I am doing a project looking at the ability for antibodies to attack certain antigens. I need the amino acid sequence of the antibody for the drug heroin, if anyone is familiar with the sequence, please let me know or let me where I can attain that sequence. Once, I get that amino acid sequence, I need to be able to develop a 3D structure of that antibody. If anyone is familiar with an online program that does that, please let me know. I also need a somewhat simple computer program that I can use to determine the binding rate of an antigen to an antibody(in this case, heroin and its antibody). Please let me know if you are aware of any programs that let me do that. Thanks

[PhilGeis]

https://pubs.acs.org/doi/abs/10.1021/jm200461m and search google scholar

[BabcockHall]

My first reaction to what you are proposing is that it is extremely ambitious for a high school project.  Although docking programs can give some indication of affinity, I am not aware of programs that provide association rate constants.

[zkhan]

I'm a high school student developing an independent research project. If something is off, please feel free to correct me; I need all the help I can got. Thank you

First of all, could somebody please confirm that this is an antibody based off the mu-type opioid receptor?

https://www.drugbank.ca/drugs/DB06317

If the antibody linked above is truly based off the mu type receptor, could I somehow alter its structure to bind to a specific antigen, such as heroin? How would I go about altering the structure, would I literally mess around with the structure or alter the amino acid sequence? How would I go about doing both of those things?

 

Also, if somehow I am able to alter the antibody to become specific to heroin and treat heroin as an antigen, how would I go about testing the binding rate of heroin to this newly developed antibody? I would need some sort of data to show levels of affinity, what programs or algorithms would I use?

 

Please feel free to add your own input; I really want to do this project, but I don't know how feasible this truly is. This is something I've become passionate about, so please, please help me if you can. 

[MaximThibodeau]

If is is has not been done yet, to confirm that hypothesis (the Drug match the opioid receptor), you will need to compare in 3D the agonist and receptor, first, because its almost free (your time), and at last try it (costly). There should be some better software than others (free and not free), to do so, but by comparing only the suspicious part by their ARN or amino sequence, you could find some clues.

Once built, those molecule, cannot be modify easily (if they can), so you will need to build an amino-acid sequence, that will be encode by ribosomes, by the well known process (i think).

Heroin trig some neuroreceptors (at least one because its really a drug), experimental data could be achieved by different ways, but one could be to scan the brain of a mouse that is trigged, by your protein. Mouse life, could be save by the use of synthetic amplifier system, that will copy the chain of reaction of the nervous cell to achieve a delta color or something easy to see, but I am alone wanting to save mouse life

Maybe you need to be more specific, I will be please to help you more if needed...

[zkhan]

I am a high school student working on an independent research project. How would I go about developing a custom antibody -it's sequence and structure- online? And if I were successful in doing that, how would I test the antigen's docking ability to the custom antibody? I understand the fact that I will need to apply for a license to use various computer software programs.

[hypervalent_iodine]

!

Moderator Note

Similar threads merged.

 

[zkhan]

3 minutes ago, hypervalent_iodine said:

!

Moderator Note

Similar threads merged.

 

I'm not able to view the replies. It says "Moderator Note

Similar threads merged."

[hypervalent_iodine]

26 minutes ago, zkhan said:

I'm not able to view the replies. It says "Moderator Note

Similar threads merged."

 

I’m not sure I understand your problem. You have made three threads on the same thing. There were a few replies. Those are now all in this one thread. 

[zkhan]

Ok, thank you