Difference between homology modelling and folding modelling
Answers
Explanation:
Computational protein structure prediction provides three-dimensional structures of proteins that are predicted by in-silico techniques. Such protein modeling relies on principles from known protein structures obtained via x-Ray crystallography, NMR Spectroscopy, as well as from physical energy functions.
There are three main methods of modeling:
The first and favorite method is Homology Modeling,1-2
Followed by the Threading/Fold Recognition method,
And last but not least the Ab-initio Method.
Homology Modeling
You only use this method with a structurally unknown protein sequence and a structurally known similar protein (over 30% identity). This method relies on programs like BLAST to search for similar proteins in protein structural databases, such as PDB (Protein Data Bank). Another term for this method is comparative modeling, because you compare the protein sequence with known template structures.
The main tool or software you need for homology modeling is MODELLER. Note, this is a Python script open software source. Currently, a GUI version of the program is available called Easy Modeller, which lets you make a model of the protein with the ease of snapping your fingers.
Threading/Fold Recognition
With this method, you can predict the protein structures of your target protein using known protein folds of similar proteins found in different databases. You can do this easily through online web servers, such as I-Tasser and others.
Ab-initio Method
This method predicts protein structures when the structural information of similar proteins is not available. The protein structures are built from scratch by calculating the most favorable energy conformations. This method should only be used as a last resort.
Of the three methods, homology modeling is the star. This is due, in part, to the current availability of a large number of experimentally determined protein structures. Although many tools and servers are available for homology modeling, the main steps you need to follow for these programs are almost the same.
The Rungs of Homology Modeling
Consider homology modeling as a ladder with some rungs. Each rung or step is important in its own way and we cannot skip a step and jump up. If we do then, our final structure may fumble or turn out to be a disaster.
Explanation:
It differs from the homology modeling method of structure prediction as it (protein threading) is used for proteins which do not have their homologous protein structures deposited in the Protein Data Bank (PDB), whereas homology modeling is used for those proteins which do.