In one of our previous articles, we explained the basic methodology involved in the homology modeling of a protein. In this article, we are going to compare the two methods of protein structure prediction: Homology modeling & ab initio prediction.
Both types of methods have their own merits and demerits. It completely depends upon your study which method you select for structure prediction.
This is the basic comparison between the widely used methods of protein structure prediction.
|Parameters||Homology Modeling||Ab initio Prediction|
|Criteria||Similarity >= 30-32%||Similarity <= 30-32%|
|Homology Search||Performed||Not performed|
|Template search||Performed||Not performed|
|Structure Quality||Depends upon the algorithm used.||Depends upon the algorithm used.|
|Most widely used Software||Swissmodel||I-Tasser|
|Advantage||More accurate if shows high similarity with the template.||More precise|
|Disadvantage||Not precise in case of low similarity with the template||
Might not be accurate.
I-TASSER: Uses & Applications
I-TASSER  is another most widely used bioinformatics software. It is used for protein three-dimensional structure modeling. In this article, we are going to discuss its uses and applications in bioinformatics. (more…)
Tutorial: Basic protein structure modeling using MODELLER
SALI MODELLER  is one of the most widely used command-line bioinformatics software for protein structure prediction based on homology modeling. The installation of MODELLER on Ubuntu has already been explained in an article published previously. This article will explain how to perform basic modeling of a protein sequence having a high percent identity with the template. (more…)
Methodology for Homology Modeling of a Simple Protein
Previously, we have explained the initial methods involved in the structure prediction of a protein. In that article, we discussed the three basic methods involved in protein structure prediction: Homology modeling, ab-initio, and threading. In this article, we will explain the methodology involved in performing the homology modeling of a simple protein. (more…)