The Answer of Mid-Term Examination

SCCH604652 – Introduction of Bioinformatics (S1) / MKI80056 – Bioinformatics (S2)

Thursday, 25th October 2018 | 10:00-11:40 WIB | Open Source
Lecturer: Prof. Dr. Usman Sumo Friend Tambunan
Assistant: Ade Hanna Natalia, S.Pd; Eka Gunarti Ningsih, S.Pd; Elsafira Ariaviani, S.Si;
Mutiara Saragih, S.Si; Satya Anindita, S.Tp; Yulianti, S.Si.

Answer from Hafidatul Wahidah (1606901804)

1. a. Pharmacoinformatics is the study, invention and effectuation of discipline where

technology with any aspect of drug delivery, from the basic sciences to the clinical
use of medications in individuals and populations. Informatics is commonly defined
as the “use of computers to manage data and information” and represents the nexus of
people, information, and technology. Includes pharmacy technologies involved in the
preparation, delivery, and management of medication use within health care delivery
systems
(Source : a vital role of pharmacoinformatics | Request PDF. Available from:
https://www.researchgate.net/publication/279996178_A_VITAL_ROLE_OF_PHAR
MACOINFORMATICS [accessed Oct 24 2018, 19.20 WIB]. )

b. Computational biology involves the development and application of data-

analytical and theoretical methods, mathematical modeling and computational
simulation techniques to the study of biological, ecological, behavioral, and social
systems.[1] The field is broadly defined and includes foundations in biology, applied
mathematics, statistics, biochemistry, chemistry, biophysics, molecular
biology, genetics, genomics, computer science and evolution

(source A. Wallace Hayes, Claire L. Kruger.2014. Hayes' Principles and Methods of

Toxicology, Sixth Edition. CRC Press : New York)

c. Biostatistics is the application of statistical principles to questions and problems in

medicine, public health or biology. The discipline of biostatistics provides tools and
techniques for collecting data and then summarizing, analyzing, and interpreting it. If
the samples one takes are representative of the population of interest, they will
provide good estimates regarding the population overall.
 (source:http://sphweb.bumc.bu.edu/otlt/MPHModules/BS/BS704_BiostatisticsBasics/
BS704_BiostatisticsBasics_print.html [ accesed Oct 24 2018, 19.25] )

d. Bioinformatics is conceptualizing biology in terms of macromolecules (in the

sense of physical-chemistry) and then applying "informatics" techniques (derived
from disciplines such as applied maths, computer science, and statistics) to understand
and organize the information associated with these molecules, on a large-scale.
Bioinformatics very useful in others knowledge, like Medical Science, the study and
application of computing methods to improve communication, understanding, and
management of medical data.

(Source: Video Bioinformatics Information by Prof. Usman Sumo F. Tambunan, Dr.

rer. Nat Arli Aditya Parikesit, Hilyatuz Zahroh, S.Si., MA on
https://scele.ui.ac.id/mod/resource/view.php?id=5113 accessed on 24 October 2018,
20.12 WIB)

(source : Luscombe NM. 2001. What is bioinformatics? A proposed definition and

overview of the field. Available frohttps://www.ncbi.nlm.nih.gov/pubmed/11552348
[accesed Oct 24 2018, 19.30 WIB] )

2. a. Forensic Field
The role and the application of Bioinformatics on
The role:
 In DNA sampling, while examining population of identical units, decision
is made on smallest population sample size and test results of statistical
importance are also influenced by Bioinformatics.
 Recognizing the microbial samples in a very short amount of time that
contains multiple levels of declaration.
 Identifying protein structure, gene composition, and also useful association
between dispersion and virulent systems.

The application:

 DNA Testing, according to Forensic bioinformatics basic task is to

make advancement in setting up the forensic records which is useful to
store rough draft of DNA of criminals that is taken from the crime
scene and later presented for DNA testing.
  Gender Identification, bioinformatics can be used to take full
advantage for forensic analysis. For gender identification, amelogenin
marker testing is required. Amelogenin being a protein that is made up
of about 90% of tooth enamel protein.
 Parentage Testing, forensic bioinformatics play crucial role in child
parental issues.

(Source: Muntaha, Sidra Tul, dkk. 2018. Role of Bioinformatics in Forensic

Science. FUUAST J.BIOL., 8(1): 133 – 138)

b. Microorganisms Taxonomy
The role: In microorganism taxonomy, bioinformatics is used for three
approaches, that is:
 Computational search and alignment techniques to compare new genome
against the set of known genes to annotate the structure and function of
genes in a newly sequence genome.
 Mathematical modeling techniques such as data mining, statistical
analysis, neural networks, genetic algorithm, and graph matching
techniques to identify common patterns, features and high level functions.
 Integrated approach that integrates search techniques with mathematical
modeling.

The application: (Source: Muntaha, Sidra Tul, dkk. 2018. Role of

Bioinformatics in Forensic Science. FUUAST J.BIOL., 8(1): 133 – 138)

 Computationally analyzing the wet-lab data.

 Genome sequencing .
 Identification of protein coding segments and genome comparison to
identify the gene function.
 The development of genomic and proteomics databases and inference
of phenotypes (higher level functions) from genotypes (gene level
functions).

(Source: Bansal, Arvind K . 2005 . Bioinformatics in Microbial

Biotechnology . USA: Kent State University accessed on
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182391/ )
3. Bioinformatic analysis can not only accelerate drug target identification and drug
candidate screening and refinement, but also facilitate characterization of side effects
and predict drug resistance. High-throughput data such as genomic, epigenetic,
genome architecture, cistromic, transcriptomic, proteomic, and ribosome profiling
data have all made significant contribution to mechanism-based drug discovery and
drug repurposing. Bioinformaticians in drug discovery use high-throughput molecular
data in comparisons between symptom-carriers (patients, animal disease models,
cancer cell lines, etc.) and normal controls. The key objectives of such comparisons
are to
1) connect disease symptoms to genetic mutations, epigenetic modifications, and
other environmental factors modulating gene expression
2) identify drug targets that can either restore cellular function or eliminate
malfunctioning cells, e.g., cancer cells
3) predict or refine drug candidates that can act upon the drug target to achieve the
designed therapeutic result and minimize side effects
4) assess the impact on environmental health and the potential of drug resistance.

( source ;Xuhua Xia. 2017. Available from:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5421137/ [ accesed Oct 24 2018,
20.35 WIB] )

4. b. Homology modelling and Ramachandran Plot; please provide the logical step to
perform homology modelling of Zika virus capsid protein sequences with accession
number:> YP_009227196.1, and how to validate the template of the protein that you
have obtained from homology modelling process, and please specify what the
requirements that can be used for the protein validation!
Main Concept of Homology modelling and Ramachandran Plot Homology
modelling refers to constructing an atomic-resolution model of the "target" protein
from its amino acid sequence and an experimental three-dimensional structure of a
related homologous protein (the "template"). Homology modeling relies on the
identification of one or more known protein structures likely to resemble the structure
of the query sequence, and on the production of an alignment that maps residues in
the query sequence to residues in the template sequence. Then, the template sequence
plotted in Ramachandran Plot to know the model of protein and to validate the
protein.

Step 1
Find the journal with accession number: YP_009227196.1 in the database at National
Center for Biotechnology Information (NCBI) through site
http://www.ncbi.nlm.nih.gov/genomes/flu/.

Step 2

After show like this picture, choose FASTA

Step 3

Copy FASTA that has been obtained

Step 4

The next step, open Basic Local Alignment Search Tool (BLAST) through the site
https://blast.ncbi.nlm.nih.gov/Blast.cgi. BLAST is a software that can be used to
determine the homology of a DNA sequence or amino acid with data that is on NCBI

Than, Paste fasta in tis Enter Query Sequence column. On the column of Program
Selection, Algorithm, give a check sign in blastp (protein-protein BLAST) square.
After that, click “BLAST”

Step 5

After blast this data, we will get the result

This is the distribution of the top 100 Blast Hits on 100 subject sequences. From this
graphic we know that alligement scores for zica virus almost in range 80-200 query.

Step 6

In Sequences producing significant alignments we choose that has identity in range 90% -
100%, and then choose that has accession number: > YP_009227196.1, and click the
accession number

Step 7
After that will show sequence of this accesion, and click FASTA
Then copy this FASTA

Step 8

Open Swiss Model, and click “Start Modelling”

https://swissmodel.expasy.org/interactive
Step 9
Paste your Fasta on the column of Target Ssequence

After that, search for templates, and they will give us the templete results of zika
virus, there is 8 templates, than choose the bigger identity (97.37) and click build
models
Step 10

We will get the homology modelling of Zika virus capsid protein sequences with
accession number:> YP_009227196.1 , and download zip to get the .pdb file

Step 11

To validate the template of the protein that you have obtained from homology
modelling process, we use Ramanchandran Plot. So the next step is open
http://mordred.bioc.cam.ac.uk/~rapper/rampage.php
On the table of Ramachandran Plot Analysis, choose file .pdb that already
downloaded before. Then, click Submit to Rampage. Wait until the result’s out.
Validate the protein.

The result will be:

Residue [A 24 :VAL] ( -71.66, 98.36) in Allowed region
Residue [A 26 :PRO] ( -97.00, 63.42) in Allowed region
Residue [B 24 :VAL] ( -30.53, 76.85) in Outlier region
Number of residues in favoured region (~100.0% expected) :
171 ( 98.3%)
Number of residues in allowed region ( ~2.0% expected) :
2 ( 0.0%)
Number of residues in outlier region :
1 ( 0.0%)

The ramanchandran plot doesn’t show in this web, so download post.script file
and open with adobe Photoshop
Ramachandran Plot of Zika virus capsid protein sequences with accession
number:> YP_009227196.1
 If a Ramachandran plot of these structures contains highly anomalous f and y
values, it can be assumed that a mistake might have occurred in the
determination of the position of atoms.

 The requirements that can be used for the protein validation are
1. Favorite region> 90% in tihs result we get 100 %
2. Allowed Region <8% in this result we get 0.0 %
3. Outlier Region <2% in this result we get 0.0 %
4. The plot results from Ramachandran correspond to the minimum limits
that can be used, then validation is successful.

So we can conclude that Zika virus capsid protein sequences with accession
number:> YP_009227196.1 was valid.

(Source: Kuno,G. and Chang,G.-J.J.2018. Full-length sequencing and genomic

characterization of Bagaza,Kedougou, and Zika viruses. accesed on :
https://www.ncbi.nlm.nih.gov/protein/YP_009227196.1/ )