Name: Ravinder

Roll no. 19111035

Experiment No. 11
AIM:
Visualization tool- PyMol & BIOVIA Discovery Studio
Visualizer.
Procedure:
 Go to PDB site https://www.rcsb.org/ and search for
1MBO in search bar.
 Go to top and download the structure of 1MBO in PDB file
format.
 The file saved itself in PDB format then click to open file it
will opened in PyMol tool.
 After opening in PyMol we will applied follows process on
file

 Manipulating the PDB file

 Customizing the PDB structure:
 Click on Display and then select Sequence. This creates
the primary structure of protein, then Go to selecting in the
corner and click on Objects.
 Select the zeroes right (click > show > spheres)

 Click<Label< Residue Name

 To remove the cartoon structures and view the stick
structures. Select the amino acid sequence> right click>
Hide> Cartoon. Then right click> Show> Stick.

 Select the zeroes right (click > show > spheres)

After removing the background we will get the below

structure
 Discovery visual:
Discovery Studio provides software applications covering the
following areas:

1. Simulations
2. Including Molecular Mechanics, Molecular Dynamics,
Quantum Mechanics
3. For molecular mechanics-based simulations: Include
implicit and explicit-based solvent models and membrane
models
4. Also includes the ability to perform hybrid QM/MM
calculations
5. Ligand Design
6. Including tools for enumerating molecular libraries and
library optimization
7. Pharmacophore modelling
8. Including creation, validation and virtual screening
9. Structure-based Design
a. Including tools for fragment-based placement and
refinement,[9] receptor-ligand docking and pose
refinement, de novo design
b. Macromolecule design and validation
c. Macromolecule engineering
d. Specialist tools for protein-protein docking
e. Specialist tools for Antibody design and optimization
f. Specialist tools for membrane-bound proteins,
including GPCRs
10. QSAR
Covering methods such as multiple linear regression,
partial least squares, recursive partitioning, Genetic
Function approximation and 3D field-based QSAR

 Process-