EL's+Milestone+-+What+is+homology+modeling+method?

d. What is homology modeling method?
 * Care must be used in applying the term, "homology modeling." In fact, as noted above some authors prefer alternative names for the procedure. One must recognize that homology does not necessarily imply similarity. Homology has a precise definition: **having a common evolutionary origin** [6,7]. Thus, homology is a qualitative description of the nature of the relationship between two or more things, and it cannot be partial. Either there is an evolutionary relationship or there is not. An assertion of homology usually must remain an hypothesis. Supporting data for a homologous relationship may include sequence or three-dimensional similarities, the relationships between which can be described in quantitative terms.

An observation of importance in homology modeling is that for a set of proteins that are hypothesized to be homologous, their three-dimensional structures are conserved to a greater extent than are their primary structures. This observation has been used to generate models of proteins from homologues with very low sequence similarities. Thus, in homology modeling, we are attempting to develop models of an unknown from homologous proteins. These proteins will have some measure of sequence similarity but we are relying on the conservation of folds among homologues to guide us as well. ||