Building a Model

The comparative modelling procedure may be split into 8 stages:

1. Identify one or more (homologous) sequences of known structure to use as "templates" or "parents"
2. Align the target sequence to be modelled with the parent(s),
3. Determine the boundaries of the "framework" or "structurally conserved regions" (SCRs) and the "structurally variable regions" (SVRs). The latter are generally loops.
4. Inherit the SCRs from the parent(s)
5. Build the SVRs
6. Build the sidechains
7. Refine the model
8. Evaluate errors in the model

Note 1: the terms "template" and "parent" are used interchangeably.
Note 2: the template structures need not be homologous if they have come from fold recognition or threading, but they generally are homologous and will almost certainly have to be homologues of high sequence identity if a good quality model is to be built.

This type of approach may be implemented manually or automated with systems such as SwissModel (over the web) or COMPOSER.