SWISS MODEL

Question 1

Explain about Swiss model, it’s key features and application with procedure

Answer 1

Definition: Swiss Model is a web-based tool for homology modeling of proteins.

Purpose: To predict 3D structures of proteins based on known structures of homologous proteins.

Usage: Ideal for researchers in bioinformatics and structural biology for understanding protein function and interactions.

Type: Web-based tool for protein homology modeling.

Function: Predicts 3D structures of proteins based on homologous templates.

Template Library: Utilizes the Protein Data Bank (PDB) for known structures.

Sequence Alignment: Automatically aligns target and template sequences.

User-Friendly Interface: Easy-to-navigate platform for researchers.

Model Refinement: Offers optimization tools for improving model quality.

Validation Tools: Includes assessments like Ramachandran plots for model quality.

Applications: Useful in bioinformatics, drug design, and structural biology research.

Procedure for Building a Homology Model:

1. Identify the Target Protein:

Determine the sequence of the protein of interest.

2. Search for Template Structures:

Use databases like PDB to find homologous proteins with known structures.

3. Align Sequences:

Perform sequence alignment between the target and template proteins to identify conserved regions.

4. Build the Model:

Use Swiss Model to construct the 3D model based on the aligned sequences and template structure.

5. Refine the Model:

Optimize the model for steric clashes and improve geometry using energy minimization tools.

6. Validate the Model:

Check the quality of the model using validation tools (e.g., Ramachandran plot, Z-score).

7. Analyze the Model:

Perform further analysis to study structural features and potential functional implications.