However, bacterial organisms often fail to produce target proteins due to problems related with protein misfolding and protein glycosilation.
Yeast and fungal protein expression systems are used for the industrial production of relevant enzymes in such cases .
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 .
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.On the last two decades the development of recombinant DNA techniques has extended the use of microbial organisms to produce target proteins.The enteric bacterium Escherichia coli is one of the most extensively used prokaryotic organisms for genetic manipulations and for industrial production of proteins of therapeutic or commercial interest [1, 2].Consequently, it is likely that at least one example of most structural folds will be known, making comparative modeling applicable to most protein sequences.In term, an essential step of structural genomics is production of target proteins.Flowchart of methods used for comparative modeling.Scheme of the methods used for comparative modeling, comprising template(s) selection, template-target alignment, model (backbone and loops) building, sidechain modeling, model evaluation, and model refinement steps.Such templates may be found by sequence comparison methods or by sequence-structure methods also known as threading methods.Sequence comparison methods can be safely used above a certain threshold in terms of sequence identity (i.e.Microbial cell factories play a key role in this context.This review is intended to give a primer addressed to scientists of disciplines related to microbial cell factories who has no expertise in comparative modeling.