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27617 Protein structure and computational biology

Danish title:

Proteinstruktur: Modeller, analyser og beregninger


Point( ECTS )


Course type:

Taught under single-course student
Technological specialization course, MSc. Eng., Advanced and Applied Chemistry
Technological specialization course, MSc. Eng., Bioinformatics Systems Biology
Technological specialization course, MSc. Eng., Biotechnology


F5A (Wed 8-12)


Campus Lyngby

Scope and form:

Lectures, computer exercises, hand-in exercises and group work

Duration of Course:

13 weeks

Date of examination:

Decide with teacher, First or second week after the course.

Type of assessment:



Recommended prerequisites:

Participants restrictions:

Minimum 10

General course objectives:

The aim of the course is to enable students to analyse protein structure and function for the purpose of rational drug design and optimization of biocatalysts. This includes practical computer exercises dealing with construction and validation of homology models of proteins for which no experimental structure is available, as this allows prediction of biological properties of novel proteins.

Learning objectives:

A student who has met the objectives of the course will be able to:
  • Reproduce the 20 natural amino acids and account for their structural and chemical properties.
  • Describe the basic protein structure elements and their properties.
  • Describe the necessary steps for determination of three-dimensional protein structures using NMR spectroscopy and x-ray crystallography, and account for essential strengths and weaknesses of the two methods.
  • Navigate the PDB structure database and the corresponding file types
  • Operate the basic functions of the program PyMOL for visualisation of protein structure.
  • Predict local structural properties of proteins based on their sequences using common, web-based prediction tools.
  • Evaluate the quality of experimental protein structures based on general validation criteria.
  • Construct a homology model of a protein of unknown structure given the sequence and evaluate its quality.
  • Analyse and discuss the structural context of annotated protein features such as epitopes, post-translational modifications and active sites.
  • Predict the effect of point mutations on the interaction with ligands, conformational changes and other structural properties.


Protein structure from primary to quaternary, experimental determination of protein structures, structural genomics, prediction of secondary structure, accessibility etc, fold recognition, homology modelling, structure validation, protein structure analysis, protein engineering.


The project work at the end of the course is performed in small, self-elected groups and presented as a poster on the last day of the course (prior to the exam). The individual, oral exam is based on the poster/project but may also cover other parts of the curriculum.

The hand-in exercises (2) deal mainly with protein structure visualization using the program PyMOL.

Green challenge participation:

Please contact the teacher for information on whether this course gives the student the opportunity to prepare a project that may participate in DTU´s Study Conference on sustainability, climate technology, and the environment (GRØN DYST). More infor http://www.groendyst.dtu.dk/english


Paolo Marcatili , Lyngby Campus, Building 208 , pmar@cbs.dtu.dk


27 Department of Systems Biology

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Last updated: 04. maj, 2015