Protein Modelling Research Papers

Protein Modelling Research Papers-87
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.

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Our goal is to provide the seeding background to understand concepts, opportunities and challenges of comparative modeling.

We will describe each step in the comparative modeling process, discuss the most common errors and how to solve them, as well as outlining the applications of comparative modeling in the field of microbial cell factories.

In this process a variety of programs and web servers can be used (Table 1).

Additionally, protein modeling meta-servers are emerging. They automatically implement the full process in a multi-step protocol, using simultaneously different methods [15].

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].

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.

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.


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