How a model structure is created

A structure model is created by mapping the query sequence onto the template structure based on a sequence alignment (see figure 17.19):

Image CreateModelAlignment_markup
Figure 17.19: Sequence alignment mapping query sequence (Query CDK5_HUMAN) to the structure with sequence "Template(3QQJ - CYCLIN-DEPENDENT KINASE 2)", producing a structure with sequence "Model(CDK5_HUMAN)". Examples are highlighted: 1. Identical amino acids, 2. Amino acid changes, 3. Amino acids in query sequence not aligned to a position on the template structure, and 4. Amino acids on the template structure, not aligned to query sequence.