I am attempting to dock two proteins and we have a general idea of the binding site on one of the proteins (protein 1) , but are unsure where the binding site of the second protein is (protein 2). We'd like to restrict the dockable area of protein 1 while leaving protein 2 unrestricted. I am trying to use the uniform trans flag. I did some testing/internet searching but I can't seem to understand exactly how its working. Here is the definition:
Uniform random repositioning of the second partner about the first partner within a sphere of the given radius, [R].
1. where is the origin of the sphere? can we change this?
2. What is the criteria/cutoffs for "within"?
May be i'm approaching this in the wrong way, any suggestions would be helpful.