IAverage Vector Distance(AVD) is a simple measure to quantify the medium distance between two protein contacts.
AVD is obtained by calculate the minimum average of the distances between the points of the Contacts Vectors:
IVTR is a way to measure how different two proteins are, based in the size difference and the average AVD of the contacts matches
VTR is obtained multiplying the average AVD and the sum of the dismatches in each protein, then divindig by the cutoff and the number of contacts in each protein, VTR has a value between 0 and 1.
The Match occurs when the AVD between two contacts is the lower possible, and are below the determined cutoff. Each contact form only one match, that are the best possible in the program conditions.
The software search for possibles matches between contacts, after, refine and select the bests matches for this reason, the bigger the input file(in number of atoms), or the bigger the similarity between then more time is taken to find all possible contact and more time is taken for the refinment.
The loading page wait up to 30 minutes for the match completish, but some times the match process takes longer, so a "Time Out" alert is showed and the user recieves a link to try to access the alignment in future.