I have modeled the 3D structures of the antibody and the antigen, now I have several antibodies against the same antigen, I am looking for tools that would tell me which antibody has the maximum affinity towards my target antigen. like antigen antibody docking.
I have been reading about this and there are so many tools and it is very confusing on which one is the best and which one would suit my need.
Depends on the molecules size and the ammount of torsion angles in them.
If you want to have a first look, try using Autodock 4.2. It is free, fast enough and easy to get the hand of using. Disadvantage is the ammount of torsion angles limited by 32 in summ of antigen and antibody. I recommend it as a good program to start with.
http://mgltools.scripps.edu/
You need to analyze and compare the hydrogen bonds and van der Waals interactions at the interface of the antigen-antibody complex.
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