BMB834: Protein structure, dynamics and modelling

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

The course builds on the knowledge acquired in: Molecular Biology and Protein Chemistry, “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.

• 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.

• 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

• 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

Planned lessons:
Total number of planned lessons: 50
Hereof:
Common lessons in classroom/auditorium: 20
Team lessons in classroom: 18
Team lessons in laboratory: 12

Common lessons 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.

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