COURSE SPECIFICATION FORM,
approved by the Academic Council 17.06.2015 (#39)
SECTION A: DEFINITIVE
Items in this section may be reviewed and developed within Schools as part of the Annual Program
Monitoring Process and in line with the Guidelines to Modifications to Programs and Courses.
1. General course information
1.1 School: Sciences and Humanities/Biology
1.6 Credits (ECTS): 8
Course Title: Structural Bioinformatics with
Course Code: BIOL 363
1.2
1.7
Laboratory
Pre-requisites: BIOL341 Biochemistry OR
Effective from: 2020
1.3 CHEM341 Biochemistry OR CSCI 235
(year)
1.8
Programming Languages
1.4 Co-requisites: proficiency in English
Programs: B.Sc. in
_______________________________________
Biological Sciences
1.5
(in which the course
Core
Elective
is offered)
2. Course description (max.150 words)
This course will provide an overview of existing information sources, computational techniques, to
validate, simulate, predict and analyze protein structures. More importantly, it will also provide
practical knowledge about how and when to use such techniques. The main aim of this course is to
familiarize students with the principals of structural bioinformatics by understanding the
fundamentals of macromolecular organization and structure, learning how macromolecules are
predicted and modeled, discuss about structure based drug design, analysis of macromolecules
using bioinformatics tools such as sequence and structural alignments, and to understand structurefunctional relationship in macromolecules. Special care will be taken to describe and learn the
techniques for experimental approaches in structural biology such as X-ray crystallography,
nuclear magnetic resonance, cryogenic electron microscopy and hydrogen–deuterium exchange.
Moreover, in depth presentation of various databases dealing with protein data will be also an
important part of this course.
3. Summative assessment methods (tick if applicable):
3.1 Examination
3.5 Presentation
3.2 Term paper
3.6 Peer-assessment
3.3 Project
3.7 Essay
3.4 Laboratory Practicum
3.8 Other (specify)
computer lab
4. Course aims
1) To understand the basic of terminology of structural biology and bioinformatics
2) Learn the fundamentals of macromolecular organization and structure and use it with the help of
bioinformatics tools to investigate and analyze protein structures
3) Predict and model the 3D structure of macromolecules as well as to use these structures in drug
design process
4) Get knowledge on resources for gathering macromolecular data such as protein databases
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COURSE SPECIFICATION FORM,
approved by the Academic Council 17.06.2015 (#39)
5. Course learning outcomes (CLOs)
5.1 By the end of the course the student will be expected to be able to:
- understand the difference structural biology and bioinformatics as well as computational
biology
- understand the fundamentals of macromolecular organization and structure
- visualise, explore and analyse protein-ligand structures using PyMOL software
- predict and model of macromolecules
- understand structure based drug design, molecular simulation and docking
- explore databases containing protein data
5.2
CLO
Program Learning Outcome(s) to
Graduate Attribute(s) to which
ref #
which CLO is linked
CLO is linked
1
2
3
2
COURSE SPECIFICATION FORM,
approved by the Academic Council 17.06.2015 (#39)
SECTION B: NON-DEFINITIVE
Course Syllabus Template
Details of teaching, learning and assessment
Items in this Section should be considered annually (or each time a course is delivered) and amended
as appropriate, in conjunction with the Annual Program Monitoring Process. The template can be
adapted by Schools to meet the necessary accreditation requirements.
6.
6.1
6.2
7.
Detailed course information
Academic Year: 2020-2021
6.3
Semester: Spring 2021
6.4
Course leader and teaching staff
Position
Name
Course Leader
Course Instructor(s)
Teaching Assistant(s)
8. Course Outline
Session
Date
(tentative)
1
2
3
4
5
Ferdinand Molnár
Schedule (class days, time):
Location (building, room):
Office
Contact information
#
7e519 ferdinand.molnar@nu.edu.kz
Topics and Assignments
Defining bioinformatics and structural
bioinformatics
Fundamentals of macromolecular organization
and structure
- Hierarchical levels of protein organization
- Protein 3D structure: Structural Levels, motifs
and folds
- Computer lab tutorial
Fundamentals of macromolecular organization
and structure
- Protein Domains and Domain organization
- Protein Folds and Fold classification
- Computer lab tutorial
Analysis of macromolecule
- Sequence and structural alignment
- Amino acid substitutions, amino acid
replacement matrices
- Computer lab tutorial
Analysis of macromolecule
- Quality of protein structures, Torsion angles
and Ramachadran plot
- Function from structure: Structure-function
relationship and analysis
Office hours/or
by appointment
appointment
Course Aims
(ref. # only,
see item 4)
1
CLOs
2
2
2
2
3
COURSE SPECIFICATION FORM,
approved by the Academic Council 17.06.2015 (#39)
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7
8
9
10
11
12
13
14
9.
1
2
3
- Computer lab tutorial
Prediction and modeling of macromolecules
- Homology and similarity of proteins, quality
assessments of homology models
- Computer lab tutorial
MIDTERM EXAM
Monte Carlo simulations
Protein folding and energetics
- Computer lab tutorial
Experimental approaches in structural biology:
Determination of macromolecular structures
- Computer lab tutorial
Structure based drug design, molecular dynamics
and docking
- Computer lab tutorial
Protein databases I
- Computer lab tutorial
Protein databases II
- Computer lab tutorial
Protein databases III
- Computer lab tutorial
FINAL EXAM
3
3
1
3
4
4
3
Learning and Teaching Methods (briefly describe the approaches to teaching and learning to be
employed in the course)
Lectures
Computer lab work sessions
Small project
10. Summative Assessments
#
Activity
1 Attendance
2 Midterm exam
3 Final exam
4 Small bioinformatics project
5 Short presentation
11. Grading
Letter Grade
Percent range
A
95 - 100
A90 – 94.9
B+
85 – 89.9
B75 – 79.9
Date
(tentat
ive)
Weighting (%)
CLOs
10%
30%
40%
10%
10%
Grade description (where applicable)
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COURSE SPECIFICATION FORM,
approved by the Academic Council 17.06.2015 (#39)
C+
70 – 74.9
C
65 – 69.9
C60 – 64.9
D+
55 – 59.9
D
50 – 54.9
F
< 50
12. Learning resources (use a full citation and where the texts/materials can be accessed)
E-resources, including,
http://pymol.sourceforge.net/newman/user/toc.html
but not limited to:
https://pymolwiki.org/index.php/Main_Page
databases, animations,
https://expasy.org/structural_bioinformatics
simulations, professional
blogs, websites, other eKeith JM Bioinformatics Volume II chapters 1, 2, 13, 14
reference materials (e.g.
video, audio, digests)
E-textbooks
Laboratory physical
resources
Special software programs PyMOL and web based software
Journals (inc. e-journals)
Text books
13. Course expectations
List the expectations of students for the course regarding the course attendance, class participation,
group work, late/missed submission of assignments.
Tolerance and non-discrimination: You have the right to have every opportunity to learn and
participate in this class. Therefore, if you have any hearing, visual, or motor limitations, please let us
know. Every effort possible to facilitate your learning will be made. Any student with a documented
disability needing academic adjustments is requested to speak directly to the student affairs office and
to us, as early in the semester (preferably within the first week) as possible. All discussions will remain
confidential.
Attendance: Attendance at lectures is mandatory. Absences from a lecture, due to illness or family
emergency, can only be formally excused by a note from a medical professional or by a documented
proof. If a student is over 10 minutes late, or if a student leaves half way through class, he/she will be
counted as absent for that class. If you are tardy for three (3) times it would be equivalent to one (1)
absence.
Classroom Behavior: The classroom is expected to be a place of learning and mutual respect. Cell
phones and other electronic devices must be shut off or be set on silent mode. Failure to do so may
result in ejection of the student from the class. Cell phones and other electronic devices should be set
on silent mode or be off in the classroom. Unauthorized use of these devices could result in your
expulsion from the class, and you will be counted as absent for that class.
Withdrawal Policy: Withdrawal forms will only be signed due to special circumstances such as
documented medical issues. Failing the course is NOT an acceptable excuse for the issuance of a
withdrawal.
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COURSE SPECIFICATION FORM,
approved by the Academic Council 17.06.2015 (#39)
Missed exams: There will be no make-up of the final exams. If a quiz is missed and NO appropriate
excuse is provided, the missed quiz will be graded 0%. If a quiz is missed and an appropriate excuse is
provided, the missed quiz will be graded based on average score of the final exam. You are allowed for
only one missed exam per semester.
Homework: To facilitate learning students must read uploaded materials on Moodle and/or other
indicated materials by a course instructor.
Electronic resources: You are expected to regularly check your Nazarbayev University email for
updates and announcements about the course. You are responsible to check out regularly your Moodle
account for updates on the happenings of the classroom.
Challenge of grade: Any challenge of a grade must occur within 1 week of receiving the score. No
reconsideration will be given after this point.
Office Hours: If you unable to attend the scheduled office hours, please schedule an appointment. This
is your time to ask questions regarding the lecture material, assignments, and grading concerns.
14. Academic Integrity Statement
Provide a statement requiring the students taking this course to abide by the University policies on
academic integrity.
Academic Integrity: Nazarbayev University and The School of Science and Technology considers
cheating (which includes plagiarism, ghostwriting, collusion or copying) to be unacceptable and
dishonest practice. Any students caught cheating will receive an automatic grade of 'F' and will be
reported to the Dean of SST for further penalties. Egregious cases, or a second offense, can result in
failure of the course. To avoid the perception of cheating, you are strongly advised to turn off your cell
phone or other communication devices (unless otherwise requested) and store it in your bag or locker.
Use of dictionaries during quizzes and exams is NOT allowed.
You may refer to the Student Code of Conduct and Disciplinary Procedures (approved by the AC on
05.02.2014), specifically, paragraphs 13-16 (plagiarism and cheating).
15. E-Learning
If the content of the course and instruction will be delivered (or partially delivered) via digital and
online media, consult with the Head of Instructional Technology to complete this section and/or
provide a separate document complementary to this Template.
16. Approval and review
Date of Approval:
Minutes #:
Committee:
Date(s) of Approved Change:
Minutes #:
Committee:
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