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Structural Bioinformatics

Homology Modeling vs ab initio Protein Structure Prediction

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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

How to generate electron density map using Pymol?

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How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.

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Software

How to install Kpax on Ubuntu (Linux)?

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How to install Kpax on Ubuntu (Linux)?

Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)

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Secondary structure

How to run do_dssp command (mkdssp) in Gromacs 2022?

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How to run do_dssp command in Gromacs 2022?

In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)

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