Docking isn't a nuclear physics concept. It is a technique in molecular physics / physical chemistry used to predict orientation etc when one molecule binds to another. Binding energy is the energy needed to pull the two components apart and separate them by an infinite distance.

Free nucleons are heavier than nucleons inside the nucleus. The mass difference is the binding energy.

Binding energy of a systems represents the energy one needs/the work one has to do in order to disassemble the object into different component parts which is held together by certain forces. In nuclear physics, binding energy is the energy one needs to break the nuclear force and to separate the nucleus into individual protons and neutrons. In the other words, the binding energy represent the difference between the masses of the nucleus and the sum of the individual masses of the nucleons.

The above definition is correct but it defines the energy required for the disassembling of the whole nucleus into free nucleons. Often we want to know not just the binding energy of the whole nucleus but the binding energy of a single nucleon within the nucleus or the binding energy of a cluster of nucleons, such as 4He. We want to know what energy is required to remove a single nucleon or a certain cluster of nucleons from a given nucleus. For this reason, I believe, it’s helpful to think in terms of the mass difference of nucleons inside the nucleus and outside.

Remember also that we can express mass either in terms of mass units or energy units. It is all the same. Thus, for instance, the mass of a free neutron is 1.675x10^-27 kg or 939.565 MeV/c^2, which can be simply written as 939.565 MeV.

If a nucleon inside the nucleus is lighter than a nucleon outside, then it is obvious that in order to move the nucleon from inside to outside you have to add the missing (or balancing) mass (or energy). This missing (or balancing) mass (or energy) is the binding energy of this nucleon. A nucleon is bound inside a nucleus because on its own it cannot increase its mass to escape.

In practice, it's a little more complicated, because the mass of a nucleon inside the nucleus depends on the type of the nucleus. So, to find out the binding energy of a single nucleon or a cluster of nucleons within a nucleus we have to analyse the following nuclear reaction:

A = (A-a) + a

where A is the original nucleus and (A-a) is the nucleus formed by removing a cluster a.

We can then use appropriate mass tables to find out masses of A, (A-a) and a, which, if you are lucky might be expressed in MeV or keV and the difference of masses on both sides of this equation will give you the binding energy of a inside A. If your table lists the binding energies of nuclei, you can find the binding energy of a in A by comparing the binding energy of A with the sum of binding energies of (A-a) and a. If your mass table expresses mass in amu (atomic mass unit) you can convert them to MeV (1 amu = 931.49 MeV).