Assignments

• 26,27,28 /10Introductory Computer Assignments

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• 29/10 Sequence alignments and databases

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• 5/11 Logos
• 5/11 Neural networks
• 5/11 Signalp

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• 9/11 Secondary structure predictions
• 9/11 Membrane predictions

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• 10/11 Pfam
• 10/11 HMMs and multiple sequence alignments

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• 16/11 Lattice models

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• 17/11 Threading
• 17/11 3d databases

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• 23/11 Phylogenetic trees

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• 24/11 Homology modelling (By xray)
• 24/11 Structure verification (By xray)

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• 16/12 Drug design

List of discussion questions for each lecture:

• Datorer,databaser och bioinformatik (GVH)
1. Describe the entries in Swissprot and in EMBL ?
2. Where can complete genomes be found ?
3. What can be searched at entrez, SRSm NCSA, BCM-sequence launcher.
• Det strukturbiokemiska perspektivet pålivsproc. (PN)
• Protein, grunder (DL)
1. 1. What is meant by primary, secondary, tertiary and quaternary structure?
2. 2. Describe the stereochemical limitations on peptide geometry and how they affect possible types of secondary structure.
3. 3. Describe a few of the secondary structure motifs that aee used to build up protein domains.
4. 4. How can helices pack together?
5. 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. 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. 2. What are the main differences between A-RNA and B-DNA?
3. 3. Describe some of the secondary structure elements unique to RNA
4. 4. Why are metal ions so important for RNA folding?
5. 5. What kinds of tertiary interactions can occur in complex RNA structures, e.g. tRNA?
• Alignments: dot-plots (EW)
1. Describe blast, fasta and dynamic programming ?
2. Describe ClustalW
• Protein- nukleinsyra interaktioner (PN)
• Secondary structure prediction
1. What is a helical wheel, how can it be used ?
2. Describe some different secondary structure prediciton methods.
3. Describe PhD ? What was new about it ?
• Struktur-funktion II
• Viktmatriser, neurala nät (HN)
1. What is matrix prosite search ?
2. What is pattern prosite search ?
3. How does the SignalP peptide recognition at CBS work ?
4. How are neural networks used in biology.
5. How are training and test sets used in neural networks
6. What are sequence logos.
• Membranproteiner:struktur, prediktion (GvH)
1. Describe some different methods to predict membrane topology.
• Pfam, HMM (ES/AE)
• Proteinveckning (GvH)
• Latticemodeller, simolering av veckning (AE)
1. Why does proteins fold (theories from Karplus and Moolt).
2. What is the HP model, how is it different from the models used by Shahknovich ?
3. Simplified protein models, what have they been used for ?
• Threading, 3D databaser (AE)
1. Desribe the 3d-1d threading method.
2. Describe the threader method.
3. Describe the energyfunction used by Sippl.
4. Describe the threading methods that use predicted information.
• Proteiner i immunsystemet (MT)
• Virusstrukturer (DL)
• Genomevolution (SA)
1. How do you create phylgenetic trees.
2. How is bioinformatics use to compare genomes ?
• Strukturjämförelse och homologimodellering (AE)
1. How is SCOP organized.
2. Discuss some problems with energy functions to be used in homology modelling.
3. Describe Modeller what are the criterias used for the energy function in modeller.
4. Describe ICM. How does the energy function differ from molecular dynamics.
5. 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