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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).In this process a variety of programs and web servers can be used (Table 1).
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.
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.
Programs and servers referring to these steps are listed in table 1.
The starting point in comparative modelling is to identify protein structures related to the target sequence and then to select those that will be used as templates.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.There are two main interests in the industrial production of proteins: i) Redefining the optimal properties of the target protein and ii) Avoiding problems of high-scale production.Knowledge of three-dimensional structure of the proteins may be helpful to redesign a modified protein.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.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.The progress of structural genomics initiatives  allow to model a large amount of protein sequences.Besides, the number of unique structural folds that proteins adopt is limited .