Ususally, these questions are fully answered by means of x-ray crystallography. These types of proteins are lodged within a particular cellular membrane, surrounded by a lipid bilayer, other proteins, and many other factors that make the membrane the dynamic structure that it is.
Computational analysis provides a way of postulating structure and, at times, behavior.
The protein facilitates transport of nucleotides, chloride, and other negatively charged species ordinarily impermeable to this membrane. It would be expected that two proteins of similar origin and function would have reasonable sequence similarity. One can then attempt to say that a conserved region of sequence that is, say for example, an alpha-helix in the known protein, is probably the same in the unknown's sequence. I will be doing some molecular dynamics and electrostatics calculations once I am happy with the a particular VDAC model. Since I had preliminary secondary structure information on human VDAC, these models were generated with that, but the mouse sequences have far more potential and I am concentrating on those.