Doctorate course exercises: Protein Engineering

1. Structure edition and alignment

2. Homology modeling

3. Yasara view. Just have a look

Doctorate course exercises: Functional Genomics & Proteomics

1.- DNA array and data Analysis

2.- Mass spectrometry and 2-D gel electrophoresis

Doctorate course exercises: Analysis of Biological Databases

Index

1.- Tools for bioinformatic

• Practice 1: HTML language.
• Practice 2: Transfer files to a remote computer.
• Practice 3: Run programs in a remote computer.
• Practice 4: Capture results from the screen.

2.- Scripting & Database Management

• Practice 1: Get or update structural information from a database: SMART.
• Practice 2: Get all pdb files from PROTEIN DATA BANK.
• Practice 3: Change all pdb file names to uppercase.
• Practice 4: Get Information for pdb files.

3.- Managing Protein Databases

• Practice 1: Try to find an alive database.
• Practice 2: Human erythropoietin (EPO) in different protein sequence databases.
• Practice 3: Searching all the protein sequences for the gene "ken and barbie" with text search tools.
• Practice 4: Different looks and tools for the same entry....
• Practice 5: Browsing a database.
• Practice 6: Search all proteins containing SH3 domains in S. cerevisiae and S. pombe.
• Practice 7: 3D structure database

4.- Managing Genomic Databases

• Practice 1: Browsing genes in genome databases.
• Practice 2: Locating genes in chromosomes.
• Practice 3: Gene ontology database: structure and validation of the data...
• Practice 4: Comparing two putative splice variants of a human gene.
• Practice 5: Predicting splice variants in the mouse.

5.- Managing Other Databases

• Practice 1: Metabolic / Enzyme databases.
• Practice 2: Polymorphisms.
• Practice 3: Publication databases.

6.- Tools: Pairwise Alignments

• Practice 1: Compare the sequences OPRM_RAT and SSR1_HUMAN.
• Practice 2: Dotplot using Dotlet.
• Practice 3: Perform a pairwise sequence alignment for the following analogous proteins at EBI.
• Practice 4: Perform a pairwise global alignment.

7.- Multiple Sequence Alignment

• Practice 1: Generate a multiple Sequence Alignment.
• Practice 2: Orthology and Paralogy.
• Practice 3: Produce a multiple alignment.
• Practice 4: Use BioEdit to identify consensus sequences.
• Practice 5: Make a MSA to align correctly the active center of kinases.

8.- Similarity Searches: BLAST and PSI-BLAST

• Practice 1: Make a similarity search with the protein insulin from D. rerio.
• Practice 2: Human dystrophyn similarity seraches.
• Practice 3: Nucleotide sequence and homology searches.
• Practice 4: Similarity searches in PIR database
• Practice 5: Database search with Blastp.
• Practice 6: Database search with Blastx.
• Practice 7: Do a PSI-BLAST using an alignment.
• Practice 8: Compare sequences and make a functional model based in homology.
• Practice 9: Try to characterize the gene Xrcc1 for DNA reparing in humans.

9.- Patterns, Profiles, and HMMs

• Practice 1: PROSITE database.
• Practice 2: PROSITE vs. InterPro.
• Practice 3. Protein function discovery.
• Practice 4. PSI-BLAST. Given the following sequence.
• Practice 5. Build a pattern.
• Practice 6. Search the Prosite pattern database.
• Practice 7. Build PSSMs with MEME.

10.- Genomics

• Practice 1: Mitochondria of various organisms use different genetic code.
• Practice 2: Identify anticodons of the cytosolic tRNA.
• Practice 3: Make restriction maps of nucleotide sequences.
• Practice 4: Retrieve DNA sequence encoding for human glucagon mRNA.
• Practice 5: Search the candidate primers of PCR for the human pro-optiomelanocortin gene.
• Practice 6: Use BioEdit to translate the human pro-optomelanocortin.
• Practice 7: Compare the CDS of human alcohol dehydrogenase isozymes with other organisms.
• Practice 8: A comercial automatic sequencer.
• Practice 9: Producing a restriction map.
• Practice 10: Translation.
• Practice 11: Designing primers.

11.- Proteomics

• Practice 1: Identify the protein.
• Practice 2: Analyze peptide fragments.
• Practice 3: Estimate amino acid properties from sequence.
• Practice 4: Compare the hydrophobicity/polarity profiles.
• Practice 5: Scan the relative mutability of the protein.
• Practice 6: Predict transmembrane topology of rhodopsin.
• Practice 7: Predict properties of human TRPV1.
• Practice 8: Tetramerization of human TRPV1 channel.
• Practice 9: Propose a hypothesis of activity.
• Practice 10: Amphipatic helices, helical wheels and Leucine Zipper.
• Practice 11: Find Protein domains/motifs.

12.- Structural Bioinformatics

• Practice 1: Editing structures with SwissPDB viewer. Structural alignments vs sequence alignment.
• Practice 2: Homology Modeling.
• Practica 3: Model Evaluation.
• Practice 4: Modeling proteins.
• Practice 5: Pymol usage.
• Practice 6: Electron density and coordinate accuracy.
• Practice 7: Recognize a fold.
• Practice 8: Secondary Structure Prediction.
• Practice 9: Predict secondary structure elements.
• Practice 10: Disorder Prediction.

13.- Creating - Updating a Database