CERTIFICATE
Name: Cyndrella Sajeev Admission number: 2021-44-111
Year: 3rd Semester: 6th
Certified that this is a bonafide record of practical work of Cyndrella Sajeev
Admn.No:2021-44-111 B.Tech Biotechnology student for the course BELB 3211
Structural Bioinformatics(2+1) during the semester of 6.
Date: Course Teacher:
INDEX
SL.NO. DATE TITLE PAGE REMARKS
NO.
1. SCOP
2. QMEAN
3. INTERPRO
4. PDB
5. PyMOL
6. RasMol
7. SWISS-MODEL
8. MolProbity
9. ProCheck
10. MODELLER
Exp No: Date:
ACCESSING THE STRUCTURAL CLASSIFICATION DATA OF A
PROTEIN USING SCOP DATABASE
AIM: To identify structural classification data of hexokinase including ancestry and details
about the domain 1V4S
PRINCIPLE: The SCOP database, or Structural Classification of Proteins, is a comprehensive
resource for classifying protein structures based on their evolutionary relationships and
structural characteristics.
Home page of SCOP
PROCEDURE:
• Access the SCOP using the URL: https://www.ebi.ac.uk/pdbe/scop/
• Seach hexokinase at the search bar
• Analyze the superfamily and family of hexokinase
• Select the domain 1V4S
• Select show ancestry
• Analyze the details about the domain
RESULTS:
Superfamily:
Family:
Ancestry:
Domain 1V4S:
Exp No: Date:
STRUCTURAL EVALUATION USING QMEAN
AIM: To evaluate and compare the following protein 3 dimensional structures of proteins using
different options available in QMEAN
a)2J3X
b)2J42
PRINCIPLE: The QMEAN database is a resource for assessing the quality of protein models
based on various geometric and statistical criteria. QMEAN, which stands for Qualitative
Model Energy Analysis, evaluates model accuracy using several different scoring functions
and provides insights into the reliability of predicted protein structures.
Home page of QMEAN
PROCEDURE:
• Access the QMEAN by using the URL: https://swissmodel.expasy.org/qmean/
• Download the structures in PDB format
• Upload the file in QMEAN by selecting the select coordinate file
• Select QMEANDisCo and submit
• Compare the 2 proteins by analyzing their local quality estimate
• Likewise select the QMEAN and QMEANBrane
RESULTS: QMEANDisCo
2J3X: 2J42:
Exp No: Date:
ACCESSING THE STRUCTURAL CLASSIFICATION DATA OF A
PROTEIN USING INTERPRO DATABASE
AIM: To identify the structural classification data for RUBISCO
PRINCIPLE: The InterPro database is a comprehensive resource for protein families,
domains, and functional sites. It integrates various protein signature databases and provides a
unified view of protein function, structure, and evolutionary relationships.
Member database includes:
CATH-Gene3D, CDD, HAMAP, NCBIfam, PANTHER, Pfam, PIRSF, PRINTS, PROSITE
profiles, PROSITE patterns, SFLD, SMART, SUPERFAMILY
Home page of INTERPRO
PROCEDURE:
• Access the INTERPRO using the URL: https://www.ebi.ac.uk/interpro/
• Search rubisco by selecting the search by text
• Select rubisco from the INTERPRO database
• Analyse the details about rubisco in the INTERPRO entry
RESULTS:
Exp No: Date:
ACCESSING THE PDB FOR 3D STRUCTURE OF PROTEIN
AIM: To identify the 3-dimensional structure of the protein with ID 2QOJ using RCSB PDB.
PRINCIPLE: The Protein Data Bank (PDB) is a crucial resource in the field of structural
biology. It serves as a repository for three-dimensional structural data of biological
macromolecules, primarily proteins and nucleic acids.
Home page of PDB
PROCEDURE:
• Access the PDB using the URL: https://www.rcsb.org/
• Search the id at the search bar
• Analyze the features of the protein
• Download the 3d structure of the protein in pdb format
RESULTS:
To download the 3d structure of the protein in PDB format
Exp No: Date:
MOLECULAR VISUALIZATION USING PyMOL
AIM:
a) To visualize the 3D structure of a protein in cartoon, mesh, surface and wire frame
model using pymol & perform the actions such as changing the molecule color,
background color, remove water, zoom next to ligand
b) To superimpose 2 proteins and access their compatibility using RMSD value.
a)
PRINCIPLE: PyMOL is a powerful molecular visualization tool widely used in the fields of
structural biology, chemistry, and bioinformatics.
Home page of PyMOL
PROCEDURE:
• Access the pymol
• Fetch the structure of ID 1A3N using the command fetch 1A3N
• To visualize in different forms select cartoon, mesh, surface and wire frame from the
show option
• Select different background colors from the display option
• Select by chains and select the color for the chains from the color option
• Select waters from the hide option
• Select next ligand from the zoom option in the menu bar
RESULTS:
Cartoon: Mesh:
Surface: Wire frame:
Background color:
Before: After:
Molecular color:
Before: After:
Remove water:
Before: After:
Zoom next ligand:
Exp No: Date:
MOLECULAR VISUALIZATION USING RASMOL
AIM: to visualize the 3D structure of the given protein in cartoon, ball and stick and wire frame
models using rasmol & to find the bond angle, bond length and torsion angle using command
line
PRINCIPLE: RasMol is a molecular visualization program primarily used for displaying and
analyzing three-dimensional structures of biological macromolecules, such as proteins and
nucleic acids. It allows users to visualize these structures in various representations, such as
ball-and-stick, ribbon, and surface models. RasMol is particularly popular in the field of
bioinformatics and structural biology because of its ability to render complex molecular data
clearly and interactively.
Home page of RasMol
PROCEDURE:
• Open the RasMol software.
• Open the pdb structure of the given protein.
• Select Backbone from the Display menu.
• Visualize the protein in cartoon, wireframe and ball and stick models by
using the Display menu.
Bond Angle
• Open the RasMol Command Line window.
• Enter the command set picking angles.
• Select three atoms and find the bond angle.
Bond Length
• Open the RasMol Command Line window.
• Enter the command set picking distances.
• Select two atoms and find the bond length.
Torsion Angle
• Open the RasMol Command Line window.
• Enter the command set picking torsion.
• Select four atoms and find the torsion angle.
RESULTS:
2J3X
Cartoons: Ball and stick:
Wireframe:
Bond angle:
Torsion angle:
Bond length:
Exp No: Date:
PROTEIN HOMOLOGY MODELLING USING SWISS MODEL
AIM: To predict and evaluate the three dimensional structure of an unknown protein using
SWISS- MODEL server.
PRINCIPLE: SWISS-MODEL is a widely used software for homology or comparative
modeling of protein structures. It allows researchers to predict the three-dimensional structure
of a protein based on its sequence and known structures of homologous proteins.
Home page of SWISS MODEL
PROCEDURE:
• Access the swiss model using the URL: https://swissmodel.expasy.org/
• Download the sequence of the protein using uniprot
• Select start modelling in the swiss model
• Paste the sequence and select search for templates
• Select the appropriate template and click build model
• Analyze the model by selecting structure assessment – local quality estimate and z score
RESULTS: fumerase
high similarity: low similarity:
Ramachandran plots:
High similarity:
General Glycine Pre-proline:
Proline:
Low similarity:
General: Glycine: Pre-proline:
Proline:
Exp No: Date:
ACCESS THE MOLPROBITY FOR THE VALIDATION OF PROTEIN
STRUCTURES
AIM: identify the quality of protein structure using MolProbity
PRINCIPLE: MolProbity is a software tool used primarily in structural biology for validating
and refining protein and nucleic acid structures. It provides a suite of validation metrics that
assess the geometry of macromolecular structures.
Home page of MolProbity
PROCEDURE:
• Access the MolProbity using the URL: http://molprobity.biochem.duke.edu/
• Fetch the protein using the id from PDB
• Select analyse geometry without all atom contacts
• Tick all the options in the universal
• Analyse result
RESULTS:
Exp No: Date:
STRUCTURE EVALUATION USING PROCHECK APPLICATION IN
PDB SUM
AIM: to evaluate the structure of protein using procheck option in PDBsum server
PRINCIPLE: ProCheck, which is a software tool used in bioinformatics for validating the
stereochemical quality of protein structures. It analyzes the geometry of protein structures by
checking parameters like bond lengths, angles, and torsion angles against standard values.
PROCEDURE:
• Access the PDBsum using the URL: https://www.ebi.ac.uk/thornton-
srv/databases/pdbsum/
• Search the ID in the PDB code
• Select links from the menu bar
• Select the procheck from the quality assessment
• Download each procheck analyses for the protein in pdf
RESULTS:
Main Ramachandran plot:
Main-chain parameters: Side-chain parameters:
Residue properties plot:
Main-chain bond lengths: Main-chain bond angles:
RMS distances from planarity: Distorted geometry:
Exp No: Date:
PROTEIN STRUCTURE PREDICTION USING HOMOLOGY
MODELLING BY MODELLER SOFTWARE
AIM: construct the 3D structure of the protein Tyrosine-protein kinase Yes (YES1) by choosing
appropriate template structure using modeller software
PRINCIPLE: The principle of a modeller encompasses several key concepts essential for
effectively representing complex systems. Abstraction is fundamental, allowing modellers to
simplify intricate details and focus on the most relevant characteristics. Representation
involves using various formats, such as diagrams or simulations, to illustrate components and
their relationships clearly. Validation and verification ensure that models accurately reflect real-
world systems and function as intended. An iterative development approach encourages
continuous refinement based on feedback and new insights, enhancing model accuracy.
PROCEDURE:
• Copy the protein sequence, whose structure needs to be deduced by homology
modeling, convert it to FASTA format.
• Run(Align) the sequence in BLASTp (against PDB structural databases) to identify the
matching sequences.
• Select the best possible matching structure (above 30-35% similarity). Download the
PDB file of this template(here: 3u4w.pdb).
• Create a PIR file of the sequence using the syntax given below. (NB. The text in () are
information, which are not to be included in the code)
• Save the PIR file and the template PDB file in a same location within desktop(working
directory).
• Open modeler and open the location of working directory.
• Run the PIR file modeller.(use code “mod10.5”(space)”(file-name; e.g. A.pir)
• Save the following codes as python file(name.py). Run the file using Modeller.
• Build model using the given code(save the code as a python script in the directory, run
using the Modeller).
• Open the log file and analyse the DOPE score. Find the model with the lowest score.
• Open the model with lowest dope score using PymoL.
• Open the template model using the code “fetch”PDB ID””
• Hide all the water molecules, spheres, sticks etc. 14. Align the modelled structure and
template, using the the code “align”modelled protein name”,”template name”.
RESULTS:
PIR format of query sequence:
Template structure (8JN8):
ALI file:
PAP file:
Log file:
Directory after modelling:
DOPE score:
1YES.B99990005.pdb is the best model
Visualisation of best model using PyMol:
1YES.B99990005: 8JN8:
Superimposed model:
