Structural Bioinformatics
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. |
Software
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.
Software
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…)
Secondary structure
How to run do_dssp command (mkdssp) 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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