Simplest Way of Protein Homology Modelling
In last couple of my posts, I have talked about simple bioinformatics methods of protein 3D structure predictions. List of those posts are given below-
Protein 3D Structure Prediction Tutorial
Now in this post, I will discuss the real life example of protein three dimensional structure prediction through infographs and bioinformatics video tutorials. Here, we will use the SWISS-MODEL for homology modelling tool. Before starting homology modeling with SWISS-MODEL, you have to following tasks in advance.
- Go to the SWISS-MODEL website and give your e-mail ID.
- After receiving you password in your inbox, log in to SWISS-MODEL my work space page. Actually your all work will be save here and you can access it anytime.
- Download the protein structure visualization software. like Swiss-PdbViewer or Rasmol. You can visulaize you protein 3D structure online also. (I will talk about it later in detail).
- Before, start your experiment first check the steps in protein comparative modeling.
You can use SWISS-MODEL in 3 different way
- Automated Mode : Give you amino acid sequences in given box and click on 'submit modelling request' button. Final protein 3D model will be send to your email inbox.
- Alignment Mode : Submit the alignment of your amino acid sequence and template sequence in given box and click on 'submit alignment' button. Your alignment must be in specific format. You can learn about common file format in bioinformatics and how to inter - convert different file format on this blog.
- Project Mode : This is the most advance way to submit the protein homology modelling job at SWISS - MODEL server. You will do all your template identification, alignment job in SWISS-pdb Viewer (a protein 3D structure viewer) and then submit the file to generated by SWISS-pdb Viewer to SWISS - MODEL for homology modelling. SO be careful before using this mode of SWISS - MODEL
1. Homology modelling video tutorial HERE
2. Terms used to explain protein structure HERE
3. Nature protocol paper of Bordoli et al. 2009 HERE
First of all, let me clear it that i am not a Bioinformatician. i am simple plant biology researcher who face problem in her daily research life and who bother to post solution of those problem on this webpage. That's it.