percentage of identical paired residues in an alignment).It has been shown that above that threshold -which is strongly dependent on sequence length, sequence homology implies structural identity .Microbial cell factories play a key role in this context.
Comparative modeling is becoming an increasingly helpful technique in microbial cell factories as the knowledge of the three-dimensional structure of a protein would be an invaluable aid to solve problems on protein production.
For this reason, an introduction to comparative modeling is presented, with special emphasis on the basic concepts, opportunities and challenges of protein structure prediction.
Its aim is to build a three-dimensional model for a protein of unknown structure on the basis of sequence similarity to proteins of known structure .
Comparative modeling relies on the fact that structure is more conserved than sequence during evolution.
Even though, below that threshold structural likeness is still possible.
Some protein pairs sharing very little sequence similarity may have become similar by convergent or divergent evolution.
All current comparative modeling methods consist of four sequential steps: template selection, target-template alignment, model building and model evaluation.
Essentially, this is an iterative procedure until a satisfactory model is obtained (Figure 1).
Therefore, similar sequences exhibit nearly identical structures, and even distantly related sequences share the same fold [7, 8].
Comparative modeling critically depends on the knowledge of three-dimensional structure of homologous proteins.