Aims
To describe methods problems and results in the analysis of the structural information in
protein and DNA sequences.
Contents
What are the data and the main problems? Pairwise comparison (alignment). Comparison of
many sequences (multiple alignment). Database search. Statistical significanse of sequence
similarities. Weight matrices for amino acids. RNA secondary structure prediction - energy
minimization (basepairing maximization) and coupled substitutions. The prediction of protein
secondary structure. The Protein Foldning Problem: Teoretical models and empirical results.
Homology modelling: given two (or more) homologous sequences, where only one of the
structures of the sequences is known, what can then be said about the structure of the other
proteins? Comparison of tertiary protein structures Comparison of RNA-secondary structures.
Combined structure-prediction and structure comparison. Docking: Does two given structures
fit into each other? Does a sequence fit a structure (threading)?
Prerequisites
Broad background in biology.
Teachers
Jotun Hein (person in charge) and invited quest lectures. For further information, please
contact: jotun@pop.bio.dk
Limit on number of attendees
24
Eksamination
Written take-home assignment.
Teaching material
Primary literature.
Additional remarks
This course is primarily organized for Ph.D. students and these will be given first priority in
cases of limited capacity. Graduate and postgraduate students that wish to audit the lectures
whitout receiving course credit are invited and encouraged to do so. Teaching is in English
except in cases where the instructors and all participants are Danish speaking.