22117 - Protein Structure and Computational Biology

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The three-dimensional structure and flexibility of proteins determine their function in biological processes. Knowledge about protein structure is used in structure-based drug design and optimization of biocatalysts. In cases where an experimental structure is not available for the protein of interest, homology modelling may be used to generate structural models for hypothesis-driven research. The goal of structural genomics projects is to map protein fold space and thus to allow generation of useful homology models for all proteins.

In this course, students will analyze protein structures using the program PyMOL. Key examples will be taken from influenza virus, where the molecular mechanisms underlying the different phases of the virus life cycle will be investigated. This will give the students a deeper understanding of protein structure analysis and knowledge about the newest techniques in homology modeling, protein engineering and directed evolution.


Current Course programme

Course contents

  • Elements of protein structure
  • Structural databases
  • Structural genomics
  • Fold recognition and homology modeling
  • Structure validation
  • Structure analysis
  • Structure visualisation (with PyMOL)

Pratical information

What: The course will be taught in English and consists of lectures and computer exercises. The students will be introduced to protein structure in general as well as a range of computational tools, methods and web-based services for the analysis and modelling of protein structures. The course is aimed at master students, but may also be relevant for bachelor students on their 5th or 6th semester as well as PhD-students. All students from DTU and other universities are welcome.

Please see the DTU Study Handbook for details regarding course #27617.

How: If you want to participate in the course, please sign up through the Studies Division - "studiekontoret" - at DTU. If you are not enrolled at the Technical University of Denmark, you have to sign up as a guest student (more information here: General Information for guest students from other Danish Universities)

Where: Lectures and exercises will take place at DTU, building 208 in room 062 (in the basement below CBS). Directions and a campus map is available here. Occasional changes to the location will be announced on CampusNet as well as in the programme.

Help: For more information, please contact: Paolo Marcatili or CBS course coordinator Dorthe Kjærsgaard.

PyMOL

In this course we will be using PyMOL for visualizing protein structures. More information and downloads can be found here.

Important

Mac users with the latest OS X version (10.10 Yosemite) might have troubles using the instructions reported above. Please follow this guide to install PyMOL using homebrew and let me know if it does/doesn't work


[another hack for Yosemite users]


[A giude to install pymol 1.8 on windows (and linux and mac as well)] thanks to Lars Bo Bjerrum and Jakob Jespersen

Course material

Presentations and exercise instructions will generally be made available on the programme page (see below). Copyrighted material will only be made available on CampusNet.

Course programme

Current

Archive:

Exams

The exam is based on 3 parts. 1. Two hand-in exercises. Students that fail to comply with this can not give the exam.

2. A Group project, to be presented at the end of the course. It is mandatory

3. An oral exam. A question on the student's work on the project and the hand-ins is to be expected.

A non-exhaustive list of typical exam questions Course27617_exam

A list of faqs on protein structure

CampusNet

CampusNet

Evaluations and Feedback

Remember that you can give running evaluations and feedback at the Bio-Evaluering debate forum.

Curriculum

See course programme.

Related Courses

Links

Amino Acids

Post-Translational Modifications of Proteins

Composite Protein Model Refinement Server

The server takes a PDB file minimises its energy using the same force field settings as CPHmodels. It only optimizes atoms belonging to proteins, i.e. ligands are not optimized. Any number of protein chains with or without chain identifiers are accepted.

Fun Stuff

Peptide words