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7 good questions and answers about "Functional site prediction"

What is a clue that you have an enzyme?

Conservated region (look at MSA) in a cleft

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?

What to be careful for when k-fold is not used for crossvalidation?

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?

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)

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