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Structural Bioinformatics

Homology Modeling vs ab initio Protein Structure Prediction

Tariq Abdullah

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Homology Modeling vs ab initio Protein Structure Prediction

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.

Basic Comparison

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%
Structural details Unknown Unknown
Homology Search Performed Not performed
Template search Performed Not performed
Template-based prediction Yes No
Structure Validation Performed 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.


 

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Software

I-TASSER: Uses & Applications

Dr. Muniba Faiza

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I-TASSER: Uses & Applications

I-TASSER [1] 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…)

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Homology Modeling

Tutorial: Basic protein structure modeling using MODELLER

Dr. Muniba Faiza

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SALI MODELLER [1] 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…)

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Homology Modeling

Methodology for Homology Modeling of a Simple Protein

Dr. Muniba Faiza

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homology modeling methodology

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…)

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