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Homology Modeling | Open Access Journals
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Journal of Morphology and Anatomy

ISSN: 2684-4265

Open Access

Homology Modeling

Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure. Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone. The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity usually imply significant structural similarity. Homology modelling has become a useful tool for the prediction of protein structure when only sequence data are available. Structural information is often more valuable than sequence alone for determining protein function. Homology modelling is potentially a very useful tool for the mycologist, as the number of fungal gene sequences available has exploded in recent years, whilst the number of experimentally determined fungal protein structures remains low.

 

 

 

Homology modeling, also known as comparative protein modeling, refers to the construction of an atomic resolution model of the "target" protein from its amino acid sequence and a three-dimensional structure test of a related homologous protein (the "matrix"). The modeling of homology is based on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment which maps the residues in the query sequence to the residues in the model sequence. Protein structures have been shown to be more conserved than protein sequences among homologs, but sequences falling below 20% sequence identity can have a very different structure. Evolutionary proteins have similar sequences and natural homologous proteins have similar protein structure. It has been shown that the three-dimensional protein structure is evolutionarily more conserved than one would expect on the basis of sequence conservation alone. The sequence alignment and model structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity generally imply significant structural similarity. Homology modeling has become a useful tool for predicting the structure of proteins when only sequence data is available. Structural information is often more valuable than sequence alone in determining the function of proteins. Homology modeling is potentially a very useful tool for the mycologist, as the number of fungal gene sequences available has exploded in recent years, while the number of experimentally determined fungal protein structures remains low.

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