INDEX

SL TITLE DATE PAGE NO REMARKS

NO
1 SWISS PDB TOOL SECTION 01/09/23

2 SWISS PDB TOOLPANEL 08/09/23

3 BUILDING LOOP REGION 13/09/23

4 SCANNING LOOP DATBASE 20/09/23

5 RAMACHANDRAN PLOT USING SWISS 22/09/23

PDB
6 WINCOOT 29/09/23

7 RAMACHANDRAN PLOT USING WINCOOT 06/10/23

8 DNA PREDICTION 11/10/23

9 RNA PREDICTION 01/11/23

10 MAJOR AND MINOR GROOVE 03/11/23

11 AUTODOCK 08/11/23

12 HDOCK 10/11/23

13 PLIP 22/11/23
Tools Section:
1) Surface:
i. Compute

ii Detect hydrophobic patches

iii Cavi es

iv Narrow Grooves
v Normal Grooves

vi Wide Grooves

2) Compute H-bonds
3) Compute Electrosta c Poten al:
Step 1: Set the poten al parameters.

Step 2: Output

4) Compu ng Energy (Force Field):

A force field consists of equa ons and parameters that define the poten al energy surface of a molecule.
The poten al energy used in a force field is composed of intramolecular and intermolecular energy
components.
5) Energy Minimiza on:
The goal of energy Minimiza on is to find a set of coordinates represen ng the minimum energy
conforma on for the given structure. Various algorithms have been formulated by varying the use of
deriva ves.
* Go to control Panel and select all the residues.
* Then go to the tools sec on and select the Energy Minimiza on.

6) Applying Transforma on on current Layer:

* Select the parameters

* Output
7) Building Crystallography symmetry :

8) Transla on along unit cell:

Breaking And Liga ng the Protein Backbones:

1) Breaking Protein Backbone
Step1: Open the PDB file in spdbv so ware(1rcy here)
Step2: Open control panel and hide the side chain and label the atoms.
Step 3: Go to build sec on and select break backbone op on.
Step 4: Then select any C-atom.
Normal
 Broken Backbone

2) Liga ng Protein Backbone

Step1: Open the PDB file in spdbv so ware(1rcy here)
Step2: Open control panel and hide the side chain and label the atoms.
Step 3: Go to build sec on and select break backbone op on.
Step 4: Then select the broken backbone C-atom.

Broken Backbone

Ligated
 SWISS PDB VIEWER
SERIAL NO. TOOLS ACTION
1 FITS THE VISUAL GROUP IN CENTRE

2 TRANSLATE, ZOOM AND ROTATE THE MOLECULES

3 MEASURES THE DISTANCE BETWEEN ATOMS

4 MEASURES THE ANGLES OF THE BOND

5 MEASURES DIHEDRAL ANGLE

6 IDENTIFY GROUPS AND ATOM

7 DISPLAY THE GROUP WITHIN A DISTANCE PICKED

8 CENTRE THE MODEL ON A PICKED ATOM

9 SUPERPOSE MOLECULES BASED ON TWONSELECTED RESIDUES

10 MUTATIING AMINO ACIDS

11 APPLYING TORSIONS

3. (MEASURES THE DISTANCE BETWEEN ATOMS)

Steps for using this tool
Step 1. Open a PDB file (For example: 1RCY)

Step 2. Hide all amino acid and select 2 consecu ve amino acids
Step 3. Select one atom from both the amino acid within which you want to find the
distance.
Step 4. It will display the distance

4. ( MEASURES THE ANGLES OF THE BOND)

Step 1. Open a PDB file (For example: 1RCY)

Step 2. Hide all amino acid and select 2 consecu ve amino acids

Step 3. Pick 3 atoms among which you want to measure the angles
Step 4. It will display the angles
5. ( MEASURES DIHEDRAL ANGLE)

Step 1. Open a PDB file (For example: 1RCY)

Step 2. Hide all amino acid and select 2 consecu ve amino acids

Step 3. Select one atom

Step 4. It will display the Omega, phi & psi angles
6. IDENTIFY GROUPS AND ATOM

Step 1. Open a PDB file (For example: 1RCY)

Step 2. Hide all amino acid and select 2 consecu ve amino acids

Step 3. Select one atom

Step 4. It will display the groups and atom
7. DISPLAY THE GROUP WITHIN A DISTANCE PICKED

Step 1. Open a PDB file (For example: 1RCY)

Step 2. Hide all amino acid and select 2 consecu ve amino acids

Step 3. Select one atom

Step 4. enter the distance, click “OK”

Step 4. It will display the group within a distance picked
8. CENTRE THE MODEL ON A PICKED ATOM
Step 1. Open a PDB file (For example: 1RCY)

Step 2. Hide all amino acid and select 2 consecu ve amino acids

Step 3. Select one atom

Step 4. It will display centre the model on a picked atom

9. SUPERPOSE MOLECULES BASED ON TWONSELECTED RESIDUES
Step 1. Open a PDB file (For example: 1RCY)

Step 2. Hide all amino acid and select 2 consecu ve amino acids

Step 3- open another PDB file.

Step 4- now select one atom from the previous PDB file and one from another PDB
file(select 4 atoms from each)
Step 5- it will impose on protein on other.
10. MUTATIING AMINO ACIDS
Step 1. Open a PDB file (For example: 1RCY)

Step 2. Hide all amino acid and select 2 consecu ve amino acids

Step 3. Select one atom

 Step 4.

11. APPLYING TORSIONS

Step 1. Open a PDB file (For example: 1RCY)

Step 2. Hide all amino acid and select 2 consecu ve amino acids

Step 3. Select one atom

 Step 4.

BUILDING THE LOOP REGIONS OF PROTEIN.

LOOP- Protein loops are pattern less regions which connect two regular secondary structures.
They are generally located on the protein's surface in solvent exposed areas and often play
important roles, such as interacting with other biological objects.

STEPS
 Open chimera so ware( UCSF chimera )
 Go to file op on and select fetch by id op on.

 In the PDB op on, fetch for 3DTC pdb.

 Then click on fetch op on.
 Then go to tools op on
 Select structure edi ng op on

 Then select model/refine loops op on

 A dialog box for choosing chain will open
 Choose any chain(chain A/ chain B) and click on ok.

 The red marked region shows the missing residues or the loop region.
Now, we will select template of the selected pdb file.
 Go to swiss model
 Click on start modelling
 Paste the FASTA sequence of 2gmv

 Add project tle and click on search for templates

 A er queuing, select the template.
 Then click on build model op on
 A er modelling is done, download pdb file of the model.
LOOP VISUALIZATION
 For visualiza on of loop region, go to pymol so ware
 Then go to file op on and select open op on.

 Select the pdb of 3dtc and the template pdb model_01.\

 A er both pdb gets displayed , go to pymol> tab.
 Write align 3dtc,model_01 in the pymol> tab and click on enter op on.

 Then go to display op on and click on sequence op on

 A er the whole sequence is displayed, look for the loop region in 3dtc.
 Select the sequence region the model_01 where the 3dtc residues are missing.
 The pink dots displayed are the loop regions.
 SCANNING LOOP DATABASE
Loop Database- is a database that includes all protein segments of a length up to 15 residues
contained in the Protein Data Bank (PDB).
STEPS
 Go to SPDBV software
 Then go to build option and select scan loop database option

 Pick 2 residues which will serve as anchor ones.

 For eg GLU98, GLN97
A er selec ng, loop database will be generated.

The currently selected loop appears in red dotted lines.

 The window gives you the name of PDB files that contain a suitable loop, the chain identifyer, the starting
residue, the sequence of the possible fragment, and the resolution (in Å) at which the structure has been
solved. Note that a resolution of 0.0Å means that the structure has been solved by NMR, whereas a resolution
of 9.99Å means that the source structure is a mode
 The header gives you the sequence of the loop you want to build, aligned with the sequence of a fragment selected from a
database of folds. The similarity score for the fragment appears under parenthesis and is computed from the PAM200
matrix.
 a Force Field score, a Mean Force Potential Score, a clash score, and the number of residues from the source loop that
have bad phi/psi angles (in other words, residues that would have phi/psi angles laying out of the allowed zones of
the Ramachandran plot)
 The clash score is the number of clashes per 1,000 atoms (including hydrogens)
 Sort the loops by energies or clashes to ease the process of identifying the best loop.
 RAMACHANDRAN PLOT USING SWISS PDB

Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several
proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and
compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and
distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

 Steps to be followed:
1. Open Swiss Pdb Reader
2. Then click on the windows
3. Then click on Ramachandran Plot.
4. Then from select click on the group property
5. There we get the option of acidic ,basic,polar,nonpolar.
6. Attach the pictures.

BASIC

ACIDIC

POLAR
NON POLAR

 Steps to be followed:
1. Open Swiss Pdb Reader
2. Then click on the windows
3. Then click on Ramachandran Plot.
4. click ‘Tools’
5. click ‘set omega/phi/psi
6. click helix, strand, others
7. put value
8. Click ok

HELIX

STRAND
 Steps to be followed:
1. Open Swiss Pdb Reader
2. Then click on the windows
3. Then click on Ramachandran Plot.
4. control panel > select group
5. click ‘select’
6. click ‘secondary structure’
7. click ‘Residues deviating from trans peptide bond’
8. put torsion cutoff > ok
9. click ‘file’> save > Ramachandran plot value
10. open file
 WINCOOT
WinCoot is a molecular graphics applica on. Its primary focus is crystallographic macromolecular
model-building and manipula on rather than representa on i.e. more like Frodo than Rasmol. Having
said that, wincoot can work with small molecule (SHELXL) and electron microscopy data, be used for
homology modelling, make passably pre y pictures and display NMR structures. WinCoot is Free So
ware.

Mousing and Keyboarding

Le -mouse Drag Rotate view

Ctrl Le -Mouse Drag Translates view

Shi Le -Mouse Label Atom

Right-Mouse Drag Zoom in and out

Ctrl Shi Right-Mouse Drag Rotate View around Screen Z axis

Middle-mouse Centre on atom

Scroll-wheel Forward Increase map contour level

Scroll-wheel Backward Decrease map contour level

Keyboard Zoom and Clip

N: Zoom out

M: Zoom in

OPEN PDB FILE

STEP 1: open wincoot so ware

STEP 2: go to file menu

STEP 3: select fetch pdb using accession code

STEP 4: enter a pdb accession code (e.g. 7KVP)

STEP 5: click on ‘get it’ op on.

The pdb structure will open like this.

Edit option
Under the edit op on, we can use some features like:

Bond colours
Step 1: select bond colours

Step 2: scroll the degree bar which will exhibit colour changes while changing the degree

Replace residue
STEP 1: select replace residue

STEP 2: write the residue name and then press on mutate op on

In the second picture, we can see the replaced residue.

Background colour
STEP 1: select background colour op on

Step 2: choose black or white

Calculate op on
Under this menu, we choose modelling op on
Modelling

Add hydrogen atom

Delete hydrogen atom

Delete side chains for active chain

Draw option
Under this menu, we can use some features like:
Representation tools
Under this option, we select
Ball and stick

Clear ball and stick

Grey carbons for molecules

Coloured carbons for molecules

Rock view on/off

By turning on the rock view, we can see the structure moving in le -right-le mo on slowly.

Spin view on/off

By turning on the spin view, we can see the structure spinning around fast.

Sequence view

We can see the nucleo de sequence above.

Stereo

There are 5 types of stereo view.

Mono

Hardware stereo

Side by side stereo

Side by side (wall eyed)

Zalman stereo
Measures op on
Residue info

Step 1: click on residue op on.

Step 2: click on an atom from the structure. It will show the informa on of the selected residue.

Distances and angles

Step 1: click on distances and angles.

Step 2: select distance, angle, torsion angle op on

Step 3: select ok

Step 4: select atoms. Then the distance will be shown in between two atoms, the angle and the torsion on
the below as shown in the given pictures respec vely.
Plane distances

Step 1: click on the plane distance op on

Step 2: click on the places where atom to be added

The purple box on the structure indicates the places.

Pointer distances

Clear atom labels

This op on is used to clear all the atom levels that have been pointed out earlier.

Validate option
Under this option, we get the Ramachandran plot
Ramachandran plot
Q. How to prediction of the 3d structure of rna structure?

Tool used : Rna fold web server

Rna fold web server: RNAcentral is a comprehensive database of non-coding RNA sequences that represents all
types of ncRNA from a broad range of organisms. RNAcentral is the world's largest RNA secondary structure
database.

INPUT : Octodon degus insulin mRNA, complete cds

RNAfold web server (univie.ac.at)

Output:

Example 2:

Input 2: Octodon degus insulin mRNA, complete cds

1. Search Rna fold webserver in the google chrome .

2. A web page appears .
3. Then search rna central.org in the google .

Output:
q. How to predict major and minor grooves in Dna ?

Tool used : 3D nus

3D-NuS (3-Dimensional Nucleic Acid Structures) is a web server for modeling and visualization of 3-dimensional
structures of right handed i) intra/intermolecular DNA/RNA duplexes with noncanonical base pairs along with their
chimeric forms & ii) RNA-DNA hybrid duplexes, iii) left handed Z-DNA/Z-RNA duplexes,

Two distinct grooves known as the minor and the major grooves form
on the opposite sides of the base pairs. The formation of minor grooves takes place where the sugar phosphate
backbones are far apart. While the formation of major grooves takes place where the sugar phosphate backbones are
close together.
Q. How to prediction of the 3d structure of dna structure?

A -DNA B-DNA Z-DNA

A DNA
1. A-form DNA was first identified from fibre-diffraction studies of DNA at ‘low’ (75%) relative humidity. More
recently, crystal studies have identified specific sequences which can adopt A-DNA type of structures .
2. A-DNA for any sequence is favoured under dehydrating conditions, and certain purine stretches will favour an
A-conformation, even in cases of higher hydration levels.
3. It appears that at least four purines (or pyrimidines) in a row are enough to set up a local A-DNA helix,
although of course certain purine stretches are more likely to form A-DNA than others.

B DNA
1. Commonly occurring DNA form in normal physiological conditions, this form of DNA is a right-handed
double helix
2. The two strands of this DNA run in two different directions.
3. They show an asymmetrical structure, with the alternate presence of major and minor grooves. It is a result of
the glycosidic bonds of a base pair not being diametrically opposed to one another
Z DNA
1. Structurally differing, this form of DNA is a left-handed double helix
2. The helical width of Z-DNA is 1.8 nm, making it the narrowest compared to the other DNA conformations
3. Its distinguishing factor is its backbone appearing as though a zigzag

q. How the structures can be valid?

Ans: These dna or rna structures can be valid by checking their molecular id and their graph plots that are drawn along
each of the given fig. For the proteins ramachandran plot can be considered .
 AUTODOCK
Auto Dock is a molecular docking software program commonly used in the field of
computational chemistry and molecular biology. Molecular docking is a computational
technique that predicts the preferred orientation of one molecule (the ligand) when bound to
another molecule (the target or receptor) to form a stable complex. This technique is widely
used in drug discovery, protein-ligand interaction studies, and other areas of molecular
research.
Requirements
1. MGL tools (https://ccsb.scripps.edu/mgltools/downloads/ )
2. CHIMERA (https://www.cgl.ucsf.edu/chimera/download.html )
3. PyMOL (https://pymol.org/2/ )
4. Binary Files (https://autodock.scripps.edu/download-autodock4/ )
Finding protein and ligand
1. Open RCSB (https://www.rcsb.org/ ) and search for the protein.

2. Select the query protein and download in PDB format.

3. Open PubChem and search for the ligand of the protein

https://pubchem.ncbi.nlm.nih.gov/
4. Click on download then 3D conformer SDF- save

5. Open 3D conformer in Chimera

6. Then click on file
7. Save PDB
8. Save the file as ligand.pdb

Identification Of Active Site Using Pymol

Step 1. Open Pymol

Step 2. Write the command fetch protein name (3DTC)

Step 3. Click on display sequence

Step 4. Select the ligand
Step 5. Click on A of selected residue and rename it .

Step 6. Click on H of 3dtc and hide water and cartoon.

Step 7. Now selected the residue and write a command show sticks, byres all
within 5 of selected residues(Vin) it will show the residues.

Step 8. Now click on A > find >polar contacts> to any atom

 Step 9. Click on L to label

Preparation of PDBQT file of protein and ligand using Auto Dock

Open Auto Dock

Preparation of target PDBQT

1. Click on file
2. Read molecule.
3. Select and open target file (3DTC.pdb)

4. Target molecule will appear on screen

5. Click on Edit
6. Click on Hydrogens
7. Click on Add

8. Click on polar only

9. Click Ok

10.Click charges
11.Add Kollman charges
12.Click OK

13.Click on grid
14.Click on macromolecules
15.Select the target protein
16.Click select molecule
17.Click OK
Preparation of Ligand.pdbqt file
1. Open Ligand
2. Click Input
3. Click Open

4. Change format from .pdbqt to .pdb

5. Select Ligand
6. Click Open
7. Click OK

8. Again Open Ligand

9. Click Torsion Tree
10.Click Detect Root
11.Again Open Ligand
12.Click Torsion Tree
13.Click Set Number of Torsions
14.Set number of active torsions between 1 to 6
15.Click Dismiss
16.Again Open Ligand
17.Click Aromatic Carbons
18.Click Aromaticity criterion
19.Click OK (* If ‘Enter angle in Degrees: 7.5’)
20.Again Open Ligand
21.Click Output
22.Click Save as PDBQT

Preparation of Grid Parameter File (a.gpf)

1. Open Grid
2. Click Set Map Types
3. Click Choose Ligand
4. Click Ligand
5. Click Select Ligand

6. Again Open Grid

7. Click Grid Box. Dimension of the grid box is 60X60X60. And cover the area of
active site.
 8. Click File
9. Click Close saving current
10.Again Open Grid

11.Click Output
12.Click Save GPF
13.Name the File name as a.gpf
14.Save a.gpf file (.gpf format)

Preparation of Docking Parameter File (a.dpf)

15.Open Docking
16.Click Macromolecules
17.Click Set Rigid Filename

18.Select Target.pdbqt
19.Click Open
20.Again Docking
21.Click Ligand
22.Click Choose
23.Click Ligand
24.Click Select Ligand
25.Click Accept
26.Again Docking
27.Click Search Parameters
28.Click Genetic Algorithm
29.Click Accept (*Using Default but we can change no. of GA runs)

30.Again Docking
31.Click Docking parameters
32.Click Accept (*Using Default)
33.Again docking
34.Click Output
35.Click LamarkianGA(4.2)
36.Name the File name as a.dpf
37.Save a.dpf file (.dpf format)

Molecular docking in windows command prompt

1. dir
2. cd <directory name>
3. autogrid4.exe -p a.gpf -l a.glg &
4. autodock4.exe -p a.dpf -l d.glg &
5. type 3dtc.pdbqt ligand.pdbqt > complex3.pdbqt(it will form the complex file)
Analysing results and Retrieving Ligand-Enzyme interaction complex .pdb
Analysing Results
1. Open AutoDock
2. Click Analyze
3. Click Docking
4. Click Open
5. Select a.dlg

6. Click Open
7. Click OK
8. Again Analyze
9. Click Conformations
10.Click Play
11.Click &
12.Click show information
13.Click this sign to observe each conformation from 1 to 5.
 HDOCK
Steps to be followed :
1. First of all we need to download a protein from rcsb pdb.

2. Then we need to search for ligands.

3. Select the ligand and paste it in pub chem to download the 3d structure of ligand in sdf format.>Then go to
chimera ucsf>open > ligand file.
4. Open 3D conformer in Chimera >Then click on file
5. Save PDB>Save the file as ligand.pdb

6. Then we will go to hdock where we need to paste the pdf file and the ligand file .
7. Then enter your respective mail id and then in the dialog box type – protein name then we will write ‘to
ligand’.>Then click on submit option .>The result will appear
9. Then we can see that in the left hand there are module nos labelled module 1,module 2, module 3
...>Download the first module .
10. Then open PLIP tool from chrome > Paste the module and clickc on OK.
11. An ion will appear which shows the binding of protein,ligand and water to it.