Question

The method used for prediction of three dimensional structure of protein from known structures of one or more related proteins

Answer 1

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Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate 3D structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3D structure of a given protein sequence  based primarily on its alignment to one or more proteins of known structure . The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis  is described as an example.

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