The EggNOG database is particularly useful for studies of: What connects proteins in STRING? Protein-protein interactions The same information as in Reactome, but this time automatically retrieved via algorithms Protein phosphorylation A combination of information from UniProt and pathway databases Beta sheets in proteins A combination of evidence from text mining, other databases and co-expression Evolution and orthology relationships of protein sequences Question 9 of 80 Time remaining: 176:58 Question 15 of 80 Time remaining: 1 You want to retrieve the three-dimensional structure of a protein at 3A^ resolution, or better. Which database will An ontology is: you use? PDB A book on systems biology STRING A dictionary and syntax that describe interrelationships of a system InterPro TrEMBL A computational method to identify proteins Question 10 of 80 Time remaining: 176:27 A list of homologues proteins Which approach will you use to identify a membrane-spanning region of a protein with a known amino acid sequence: Question 16 of 80 Time remaining: 174:26 Identify protein regions with closely spaced Trp residues We often take the logarithm of the measured peptide and protein intensities. Why is that? "Sliding window" method to identify regions with overrepresentation of hydrophobic residues The dynamic range of the values. Many peptides and proteins lowly abundant, very few are very highly abundant and Identify N-glycosylatien sites by searching for NxS/T sequence motifs thus stretch the displayed range. "Sliding window" method to identify regions with overrepresentation of hydrophilic residues The values are exponentially distributed To avoid having values that are zero (log (0) is -infinity)