What is Homology?
Homology is a computer program package that helps you build the structure of a protein when you know only its amino acid sequence and the complete atomic structure of at least one other reference protein. 
The reference protein (also called the real protein) can be in read in any format by MSI's interactive molecular graphics program, Insight II. The reference protein must be structurally homologous to the model protein you are trying to build (also called the unknown or sequence protein). Structural segments are taken directly from the reference protein in regions which are thought to be conserved within the family of homologous proteins. 

Homology is especially suited to situations where more than one reference structure is available. In these cases, sequence similarities alone need not be used to determine what portions of the proteins are conserved. Instead, the 3D structures themselves can be used to give a reliable prediction of the areas expected to have similar conformations. Wherever the reference proteins are found to have conserved conformations, the unknown protein is assumed to have the same conformation as well.

Homology is a collection of tools that leads you through the process of building a protein by homology. Homology is not designed to be a "black box" program for assembling purely hypothetical structures. Instead, it provides you with the ability to build a model that is chemically and physically reasonable. 

With Homology you can: 

1. Search protein databases for proteins similar to the model protein you are building.

2. Display and align amino acid sequences.

3. Find structurally conserved regions (SCRs) in reference proteins.

4. Propose structures for the loops or variable regions (VRs) between the SCRs.

5. Copy coordinates from the reference proteins to the model.

6. Refine the newly built structure using the molecular mechanics and dynamics facilities available in MSI's molecular simulation program, Discover.