Functional site prediction
7 important questions on Functional site prediction
What is a clue that you have an enzyme?
Name some types of functional sites. Why focus on active site prediction?
- Catalytic residues (in enzyme active sites).
- Specificity determinants
- Allosteric sites
- Protein-protein interaction interfaces
- Post-translational modification sites (e.g., phosphorylation, glycosylation, etc.)
For active site: you have a lot of manually curated data.
Why do you need positive and negative training data?
- Positive = residue labeled that it is catalytic
- Negative = residue labeled as definitely not catalytic
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What to be careful for when k-fold is not used for crossvalidation?
- What ended up in test set could be really easy
- or related to training set
Tell about the originial CSA dataset.
- Original hand-annotated entries, derived from the primary literature. References for these entries are given.
- Homologous entries, found by PSI-BLAST to one of the original entries (using an E-value cutoff of 0.00005).
- The equivalent residues, which align in sequence to the catalytic residues found in the original entry, are documented.(note: they check for agreement at these sites)
- KS comments: –The second type of entry is a form of annotation transfer(you should understand the fundamental assumption underlying this approach
What information is known on active sites from 3D?
- Most often in pockets/clefts
- Solvent accessible
- Must be somewhat accessible (otherwise can’t interact with a substrate!)
- Surprisingly, they are not always highlyaccessible (see Bartlett review with results of B-factor analysis)
- Secondary structure: More often on loop regions
What is the motivation for INTREPID?
- Biologists are typically interested in a single protein, not the whole family
- Not all proteins in large diverse families use all positions identically
- Active sites may be perfectly conserved, but other key positions are more likely to vary across subtypes
- Structural divergence and alignment errors will contribute noise
The question on the page originate from the summary of the following study material:
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