27617 Protein structure and computational biology
|Proteinstruktur: Modeller, analyser og
Point( ECTS )
Taught under open university
|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)
Scope and form:
|Lectures, computer exercises, hand-in exercises and group
Duration of Course:
|Decide with teacher, . First or second week after
Type of assessment:
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 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.
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
- 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
- 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
- Predict the effect of point mutations on the interaction with
ligands, conformational changes and other structural
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
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
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Last updated: 22. august, 2014