Bioinformatics Virtual Lab III

In this virtual lab, one will study the computational analysis of proteins. This lab is targeted towards PG students with exercises that will allow one to learn visualising proteins in 3D, how to calculate distance among atoms, find active sites in protein structures and also delve into some structural analysis methods including docking and homology modeling. Combining labs 1, 2 and 3 will give an overall understanding of commonly used computational methods in bioinformatics.

Visualizing the Secondary Structure of a Protein
Secondary structure of a protein is important to predict the function as well as to find out evolutionary relationship. Secondary structures thus plays an important role and can be visualized through different tools in form of cartoons, tubes, etc..
Calculating the Distance between the Ligand and a Particular Amino acid
To find out the distances between the Ligand and a particular Amino aid using PyMol.
Finding the Active Site Pockets of a given Protein Molecule
Active site pockets of a protein molecule are important , where the potential ligand molecules bind to a protein. which can be visualized through different visualization tools.
Primary Structure Analysis of a Protein Using ProtParam
To introduce a method to perform primary structure analysis of proteins which includes the computation of various physical and chemical parameters.
Secondary structure analysis of a protein using SOPMA
The Self-Optimized Prediction method With Alignment (SOPMA) is a tool to predict the secondary structure of a protein.
Surface Analysis of a Protein Using CASTp
To locate, measure and characterize the pockets located on the protein surfaces and the voids in the interior of proteins using the online resource CASTp (Computed Atlas of Surface Topography of proteins)
Retrieving details of a drug molecule
To find the structure and activity of drug molecule.
Converting chemical file formats
To convert chemical file formats according to the different platform.
Homology Modeling using Modeller
Homology Modelling is the process of predicting structure from a given protein sequence using modeling software such as Modeller.
Protein- Ligand Interaction
To carry out docking studies on the Protein-Ligand Interaction

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