Assignments
Here is a list of students who passed the assignments.
List of discussion questions for each lecture:
- Datorer,databaser och bioinformatik (GVH)
- Describe the entries in Swissprot and in EMBL ?
- Where can complete genomes be found ?
- What can be searched at entrez, SRSm NCSA, BCM-sequence launcher.
- Det strukturbiokemiska perspektivet pålivsproc. (PN)
- Protein, grunder (DL)
-
1. What is meant by primary, secondary, tertiary and quaternary
structure?
-
2. Describe the stereochemical limitations on peptide geometry and how
they affect possible types of secondary structure.
-
3. Describe a few of the secondary structure motifs that aee used to
build up protein domains.
-
4. How can helices pack together?
-
5. What are the main classes of protein fold? Can you name any
well-known proteins which have these folds?
- DNA-RNA, grunder (DL)
-
1. Describe the chemical differences between RNA and DNA. What
consequences do these have for the structure and how are they related to
the function?
-
2. What are the main differences between A-RNA and B-DNA?
-
3. Describe some of the secondary structure elements unique to RNA
-
4. Why are metal ions so important for RNA folding?
-
5. What kinds of tertiary interactions can occur in complex RNA
structures, e.g. tRNA?
- Alignments: dot-plots (EW)
- Describe blast, fasta and dynamic programming ?
- Describe ClustalW
- Protein- nukleinsyra interaktioner (PN)
- Secondary structure prediction
- What is a helical wheel, how can it be used ?
- Describe some different secondary structure prediciton methods.
- Describe PhD ? What was new about it ?
- Struktur-funktion II
- Viktmatriser, neurala nät (HN)
- What is matrix prosite search ?
- What is pattern prosite search ?
- How does the SignalP peptide recognition at CBS work ?
- How are neural networks used in biology.
- How are training and test sets used in neural networks
- What are sequence logos.
- Membranproteiner:struktur, prediktion (GvH)
- Describe some different methods to predict membrane topology.
- Pfam, HMM (ES/AE)
- Proteinveckning (GvH)
- Latticemodeller, simolering av veckning (AE)
- Why does proteins fold (theories from Karplus and Moolt).
- What is the HP model, how is it different from the models used by Shahknovich ?
- Simplified protein models, what have they been used for ?
- Threading, 3D databaser (AE)
- Desribe the 3d-1d threading method.
- Describe the threader method.
- Describe the energyfunction used by Sippl.
- Describe the threading methods that use predicted information.
- Proteiner i immunsystemet (MT)
- Virusstrukturer (DL)
- Genomevolution (SA)
- How do you create phylgenetic trees.
- How is bioinformatics use to compare genomes ?
- Strukturjämförelse och homologimodellering (AE)
- How is SCOP organized.
- Discuss some problems with energy functions to be used in homology modelling.
- Describe Modeller what are the criterias used for the energy function in modeller.
- Describe ICM. How does the energy function differ from molecular dynamics.
- What are the major differences between ICM and Modeller ?
- Motorproteiner(OL)
- Cellsignallering (PN)
- NMR1 (AG)
- NMR2 (AG eller PK)
- EM (US)
- Kristallografi 1 (MT)
- Kristallografi 2(PN)
- Kristallografi 3 (PN)
- Kristallografi 4 (DL)
- Strukturbaserad drug design (ME)
- Bioenergetikproteiner (PB)
- Metaller,kofaktorer (PN)
- Proteindesign (BMS)
- Tidsupplöst kristallografi (JH)
- Läkemedelsutv. (MN)
- Genomics
Arne Elofsson
Last modified: Thu Nov 19 15:19:00 CET 1998