Template talk:Protein domains

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Domains Resources

• NCBI's Conserved Domain Database
• Protein domains database for SWISS-PROT
• PROSITE database of protein families and domains
• EMBL InterPro database of protein families
• Pfam protein families database

Beta barrels

Nice new template! I noticed separate entries for up-and-down barrel, greek key barrel, and jelly roll barrel - these are all collectively discussed in the beta barrel article at the moment. Any opinions on splitting the article vs narrowing the template? Opabinia regalis 03:18, 16 August 2006 (UTC)[reply]

I agree, it seems very sensible to unite the various topologies under beta barrel.

I'm concerned, however, by some elements in the template that are not structural domains, in the sense that they do not fold cooperatively as a unit, e.g., the alpha helix. I started a new template Template:Protein secondary structure to cover some of those (please add some more!), but I didn't want to delete the entries here until we reach consensus.

More generally, I'm wondering about our definition of "domain". Does it mean a protein fold (i.e., a common structural architecture, such as ferredoxin fold or globin fold) or is it defined by having both a common structure and function (say, ATP-binding)? If the former (i.e., if our definition is purely structural), would it make sense to relabel the template as "Protein folds"? Just a stray thought, Willow 07:44, 16 August 2006 (UTC)[reply]

I wondered about the inclusion of secondary structures but thought there might be some use in keeping all the "protein stuff" together. Would it be too huge to list secondary structures, supersecondary structures, and folds/domains under three separate headers on the same template? I think it might be too big for lower resolutions, so the current separation works. Maybe there's a good way to provide a standard link from one template to the main article of the other.

My bias is to use "Protein folds" and keep the definition structural rather than partly functional. Even variant Rossman folds can do things other than bind nucleotides, for example, so maintaining a functional definition might be difficult. Also, if a common function were required, we'd have to find somewhere else to put things like beta propellers that don't really have one. Opabinia regalis 00:53, 17 August 2006 (UTC)[reply]

Hi, O, I've been tinkering with some templates, making them into a series: Template:Protein primary structure, Template:Protein secondary structure, etc. What do you think? They're nowhere near done, of course.

As an aside, might we want to clone this template to make a "Protein interaction domains" template? If you count up the common modular protein-protein, protein-DNA and protein-sugar interaction domains (no enzymes!), there's probably enough to fill out a good-sized template box. The protein-protein domains alone might fill such a box.

Hoping all's well with you and kitty, Willow 19:24, 17 August 2006 (UTC)[reply]

The cat's doing better at staying off the computer but my couch is taking a beating :)

I like the linked-templates idea a lot; it would make this stuff a lot more navigable. I did make a minor formatting change to the arrows. I think the primary structure one is a little long right now, especially with the two or three other navboxes at the bottom of most of the amino acid articles. Maybe it would be easier to list "N-linked", "O-linked", and "other" modifications? I'm surprised there isn't a list of standard amino acids type of page (unless I've just missed it?) but if it did exist it could contain basic data, including possible modifications, all in one place.

Template:Protein structure determination also seems a bit overcategorized to me. Maybe split it into general methods of study and actual structure determination (ie, segregate things like HD exchange and light scattering from atomic-resolution methods like crystallography). Also cryo-EM isn't necessarily only medium resolution - electron crystallography is awesome with 2D arrays of membrane proteins. Opabinia regalis 01:36, 18 August 2006 (UTC)[reply]

Hi, O, I'm a little harried at the moment (harvest time is beginning), but I just wanted to drop you a note. For Template:Protein primary structure, I wasn't thinking of using the template on every amino acid page, just on Primary structure, Posttranslational modification and the individual ptm pages such as Deamidation — does that seem reasonable? I agree we should make a special, much smaller one for the naturally occurring amino acids. For Template:Protein structure determination, I did include electron crystallography on the top line; the cryo-EM on the 2nd line was intended to be real-space microscopy, a la Keiichi Namba, Eva Nogales or Wah Chiu, those 5-10 Å structures of viruses and whatnot. I like the old-fashioned low-resolution methods, so I would kind of mourn their loss ;), but I'm open to other ideas. Template:Protein structure determination could go on the structure determination pages listed there; is that OK with you? Oops, gotta run to the stove, Willow 01:56, 20 August 2006 (UTC)[reply]

Hi again, I added a Template:Amino acids before realizing that there already was a Template:AminoAcids — oops! I also added the amino-acid propensities to Template:Protein secondary structure, which seemed a little thin; how does that look to you? Willow 11:07, 20 August 2006 (UTC)[reply]

Harvest time? Wow. I don't know what you're harvesting but it sounds yummy all the same. I think secondary structure looks good, though there might be some ambiguity eventually separating "supersecondary" from "motif" from "fold". I'm trying to fix a minor formatting issue that come up in Template:Protein tertiary structure and more seriously in my attempt to add a primary structure link to the existing Template:AminoAcids - if there's a link in the middle of the bottom navigation row, it doesn't align properly in the center of the template using the "each set of links gets its own table column" method. You seem more knowledgeable about formatting than I am (I'm terminally hopeless at anything to do with GUIness) - I've copied them into User:Opabinia regalis/aminoacids and User:Opabinia regalis/tertiary if you want to take a look without poking the real template. Do you know of a way to force the columns to evenly distribute without breaking word wrap?

Secondary structure looks good to me. I guess what we really need for the tertiary structure case is a better article on electron crystallography. Other than that everything looks great. Opabinia regalis 02:15, 21 August 2006 (UTC)[reply]

The formatted versions in my userspace do exactly what I was trying to do, so I've put those versions into the main templates. Did I mention that you're awesome? Opabinia regalis 02:19, 22 August 2006 (UTC)[reply]

And did I mention that you rock, too? Infinite praise loop! ;)

Normally, I get awkward and self-conscious when people say kind things about me, rather than my work, but the kindness of the last few days have been like sweet water on parched earth. There's been a difficult debate at Talk:Photon. It's been a good mental exercise to refine all of our understandings, but sometimes there's been more heat than light, and hardly anyone seems to cite scientific references. I confess, I feel the temptation to do the same: "See, this 5-eyed worm says that I'm awesome, so you all should go along with whatever I say." ;) Willow 11:54, 22 August 2006 (UTC)[reply]

No light at the photon article? That's not a good sign. And five-eyed worms are always authoritative on who is awesome and who isn't. You can't tell from the fossils but one of those eyes is specialized for awesomeness detection. Opabinia regalis 03:13, 24 August 2006 (UTC)[reply]