In simple words, let's say you have a protein molecule "A" that is a newly found protein, or it is a protein that is difficult to purify ( proteins are super-duper tough to purify, ufff I wish they weren't ), then we try finding a similar protein molecule to this molecule, say "B", and based on the structure of B, we try to develop the structure of A. Now, I agree that the structure might not be absolutely correct, but it still helps us understand what the structure of A could look like, and further study its properties. Now typically in homology modelling, you call the protein "A" a target protein, because that is what we are targeting to find the structure of, and we call "B" a template protein because it is a template to build our target structure on it.
Introduction to Molecular Modelling: Part 9 (Partial Charges)
In chemistry, there are ions and neutral molecules. Ions have a total positive or negative charge, while neutral molecules are often polar. The polarity…