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BMB834: Protein structure, dynamics and modelling (Structural Bioinformatics) (5 ECTS)

STADS: 01015601

Level
Master's level course

Teaching period
The course is offered in the spring semester.

Teacher responsible

Email: jenseno@bmb.sdu.dk

Timetable

Group	Type	Day	Time	Classroom	Weeks
Common	I	Monday	10-12	U146	6
Common	I	Monday	16-18	U143	9
Common	I	Monday	14-16	U155	18
Common	I	Monday	08-10	U155	20
Common	I	Tuesday	14-16	U146	8
Common	I	Tuesday	14-16	U143	11
Common	I	Tuesday	14-16	White Lab	12
Common	I	Tuesday	08-10	U143	15
Common	I	Tuesday	12-14	U143	16
Common	I	Tuesday	10-12	U17	19
Common	I	Wednesday	10-12	U68	6
Common	I	Wednesday	16-18	White Lab	9
Common	I	Wednesday	14-16	U29A	17
Common	I	Wednesday	12-14	U23A	18-19
Common	I	Wednesday	12-14	U26	20
Common	I	Thursday	12-14	White Lab	16
Common	I	Friday	08-10	U68	5
Common	I	Friday	08-10	U143	8
Common	I	Friday	08-10	White Lab	11
Common	I	Friday	10-12	U26A	18

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Prerequisites:
None

Academic preconditions:
Students taking the course are expected to:

Have basic knowledge of chemistry, biochemistry and molecular biology, including protein biochemistry and protein structure
Knowledge of basic computational approaches in bioinformatics
Use computers to retrieve data and software from public repositories

Course introduction

Detailed understanding of protein structure and function is a prerequisite for unravelling biological systems and molecular networks, and for development of new drugs for treatment of diseases.

The aim of the course is to enable the student to understand protein structure and related computational techniques to investigate protein structure. This is important in regard to protein function in biological systems, understanding protein interactions, design of protein-targeting drugs and protein-based drugs, and optimization of enzyme activities.

The course builds on the knowledge acquired in:Molecular Biology and Protein Chemistry (BMB832, Conversion class) (or similar) “Fundamentals of bioinformatics” (DM847), Introduction to programming (DM857) (or similar).

The course provides an academic basis for conducting computational protein structure analysis, and for studying protein structure-function relationships using computational tools, including macromolecular modelling methods that are part of the degree.

In relation to the competence profile of the degree it is the explicit focus of the course to give the competence to:

Acquire knowledge within the field of structural biology, protein structure and simulation
Understand and apply common terms and parameters in the context of protein structure analysis
Interpretation of experimental data using computational methods within the field of protein structure and dynamics
Understand principles of bioanalytical methods for measurements of protein structure and for determining structural constraints, including X-ray diffraction, NMR spectroscopy, mass spectrometry, calorimetry, scattering, cryoelectron microscopy
Understand basic principles and applications of High-performance computing for protein structure modelling and simulation
Perform simple protein structure modelling/simulation experiments using computational tools and be familiar with the underlying theory

Give skills to:

Embark in studies of protein structure and function using computational resources and tools.
Read and understand scientific literature on protein structure modelling and simulations
Select and apply proper computational tools for investigations of specific aspects of protein structure

Give knowledge and understanding of the importance of protein structure-function relationships in the context of biology, biomedicine and drug development

Expected learning outcome
The learning objectives of the course is that the student demonstrates the ability to:

Use scientific terminology to describe protein structure and protein structure-function relationships, and be able to present this information in written reports, discussions and presentations.

Describe the biochemical forces underlying protein folding, stability and interactions.
Describe the bioanalytical methods presented in the course.
Describe the computational methods presented in the course.
Apply computational methods for protein structure retrieval and visualization.
Apply High performance computing (HPC) methods for protein structure modelling
Describe docking methods for studying protein-ligand complexes
Apply the methods to simple problems presented in the course.
Apply the methods to situations different from the ones presented in the course;
Reflect on and assess design of computational pipelines for protein structure analysis.
Learning methods and report the results.

In relation to the competence profile of the degree it is the explicit focus of the course to give the competence to:

Appreciate the importance of protein structure analysis in biology, biomedicine and in drug development and optimization
Critically assess and select appropriate computational tools for protein structure analysis
Apply simple computational methods and algorithms to investigate protein structure and protein-ligand interactions

Subject overview
The following main topics are contained in the course:

Fundamentals of protein biochemistry and protein structure
Protein structure databases
Algorithms and computer software for protein structure analysis
Data visualization methods
Bioanalytical techniques for protein structure analysis
Protein interactions
Aspects of High performance computing
Molecular mechanics methods for protein modelling
Analysis of molecular mechanics trajectories. Constraint based protein modelling
Docking
Homology modelling

Literature
There isn't any litterature for the course at the moment.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam

Mini-projects and reports during the course. Pass/fail. Internal marking.

Assessment and marking:

Final oral exam based on review of scientific article and topics/reports prepared during the course. Internal marking, 7-mark scale. All exam aids allowed. (01015602).

Expected working hours
The teaching method is based on three phase model.
Intro phase: 20 hours
Skills training phase: 30 hours, hereof:
- Tutorials: 18 hours
- Laboratory exercises: 12 hours

Educational activities

Reading text book
Reading articles
Discussions in groups
Preparation for computational exercises / programming
Mini-projects

Educational form
The teaching follows the three-phase model. The intro phase consists primarily of lectures which will introduce the students to the general topics and themes within protein structure and structure analysis with computer and software algorithms. The tutorials and lab exercises (computer exercises), will follow up on the lectures/intro phase and will go into depth with a number of examples. The students will here work with specific problems and questions, and are expected to formulate hypotheses. The students are expected to work independently, either individually or in smaller groups. The study phase consists of preparation, reading scientific papers and writing mini projects.

Language
This course is taught in Danish or English, depending on the lecturer. However, if international students participate, the teaching language will always be English.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.