Re: Glossary terms: questions.

Lesley West (
Tue, 18 Apr 95 19:44:22 GMT


The listserver bounced my mail I wrote on 14Apr95. So here is another
try: wrote:

> 1) pKa: I assume this refers to the pH at which the half the carboxy
> of a given amino-acid are protonated. How about pKb and pKc?
> (for the amino group, and for those amino-acids
> with proton accepting/donating residues). I suggest this entry be amended
> simply to pK. The info concerning a.a's specifically will be included in
> definition.

Yes, I agree with amending pKa-c as pK (and have set this up for you
to complete).

> 2) Phosphate: phosphoryl group or phosphate (organic) sounds better. After
> all, we biochemists aren't dealing with the atom as such, but with

A note of caution here. There are a number of chemical group entries.
Once you make a rule as suggested, you have to apply it consistently
throughout. Also, the MESH headings from which Entrez is derived does
contain PHOSPHATES etc. So, go ahead and use 'phosphoryl group (or is it
radical?)' in your description but careful of making up naming conventions
that impact on other entries.
> 3) What's a pir?
See PeterMR's reply of 13Apr95. Maybe useful to add a PIR URL. Does
anyone know the URL?

> 4) predict: a bit to vague and inclusive a definition for my taste.
> Predict (structure) perhaps?
Yes, I shall delete the predict entry. However, we may find the course
turns up some predict structure gems that we want to enter in the glossary

Lesley West for PPS-glossary team