Talk:Circular permutation in proteins/GA1

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Note to reviewers: This article was written as part of PLoS Computational Biology's new Topic Page feature. The article was drafted on the PLoS topic page wiki, then peer reviewed and published on PLoS Comp Biol. Whilst I've nominated this article in its own right, I'd also appreciate any feedback as to how these Topic Pages can be closer aligned with WP guidelines.

Reviewer: Sasata (talk · contribs) 05:49, 20 September 2012 (UTC)[reply]

I'll review this. Will need a few days to read carefully (and juggle other things). Sasata (talk) 05:49, 20 September 2012 (UTC)[reply]

Comments. Here's are some comments from a quick readthrough. I'll do a literature check and check compliance with criteria 2 and 3 soon. Sasata (talk) 17:23, 27 September 2012 (UTC)[reply]

Thanks very much. I'll get to work on your suggestions. U+003F? 08:12, 28 September 2012 (UTC)[reply]
  • link protein (lead sentence); antigen presentation
 Done U+003F? 08:29, 28 September 2012 (UTC)[reply]
 Done I went with the specific, undeveloped link U+003F? 09:27, 29 September 2012 (UTC)[reply]
  • the lead currently doesn't function as a good summary of the article contents. See WP:Lead.
 Done I think this is a little better. U+003F? 17:56, 3 October 2012 (UTC)[reply]
  • It's a little short. How about adding the following to achieve a more complete summary:
  • the first circularly permuted protein was concanavalin A
  • the two main models proposed to explain the origin of these proteins
  • a sentence or two summary of the uses of circ perm in protein engineering
  • a sentence or two summary about the types of algorithms used for detection. Sasata (talk) 07:26, 5 October 2012 (UTC)[reply]
 Done Excellent suggestions. Any better? U+003F? 15:14, 5 October 2012 (UTC)[reply]
  • "This method allowed for permutations to be introduced at arbitrary sites, and is still used today to design circularly permuted proteins in the lab." source?
 Done Couldn't find a ref for the second half of this statement – removed. U+003F? 14:37, 3 October 2012 (UTC)[reply]
  • "Saposin and swaposin were the first known case of two natural genes related by a circular permutation." source?
 Done U+003F? 10:03, 30 September 2012 (UTC)[reply]
  • "The Circular Permutation Database[8] contains 2,238 circularly permuted protein pairs with known structures, and many more are known without structures." I imagine this number will change, so perhaps "As of" would be useful here. Also, there shouldn't be an outgoing link in the article text.
 Done U+003F? 09:27, 29 September 2012 (UTC)[reply]
  • Citation for the "exon shuffling" mechanism?
 Done U+003F? 10:22, 30 September 2012 (UTC)[reply]
  • In the "permutation by duplication mechanism" image (and accompanying text), it's not clear to me how the insertion of start/stop codons would cause the order of the genes to be swapped. Also, what does the "in place" part of "First, a gene is duplicated in place." mean?
 Done Make more sense? U+003F? 14:37, 3 October 2012 (UTC)[reply]
  • Much better! I added an additional clarification. Sasata (talk) 07:26, 5 October 2012 (UTC)[reply]
  • "For a review on functional and structural features of saposin-like proteins, see Bruhn (2005).[17]" This type of reference isn't usual for a Wikipedia article. More common would be to put this in this "Further reading" section, or even better, to use the article as a source and cite it directly.
 Done I pulled this sentence (but kept the reference). U+003F? 14:37, 3 October 2012 (UTC)[reply]
  • "Both consist of 4 alpha helices ..." spell out numbers less than 10, per WP:MoS
 Done U+003F? 08:29, 28 September 2012 (UTC)[reply]
  • possibly useful links: ortholog; phylogenetic analysis; restriction enzyme; ligase; substrate specificity; protein folding; calmodulin; florescence; protein topology
 Done U+003F? 09:27, 29 September 2012 (UTC)[reply]
  • not sure if the wiktionary link to "fission" is that useful
 Done U+003F? 08:29, 28 September 2012 (UTC)[reply]
  • "less accessible termini" -> "less-accessible termini"
 Done U+003F? 08:29, 28 September 2012 (UTC)[reply]
  • would like to see citations for the first paragraphs of "Algorithmic detection of circular permutations
 Done U+003F? 14:37, 3 October 2012 (UTC)[reply]
  • suggested wikilinks in the table: dot plot; geometric hashing; Ramachandran sequential transformation (is Ramachandran plot relevant?)
 Done U+003F? 12:22, 29 September 2012 (UTC)[reply]
  • the "See also" link to cyclic permutation is redundant, as it is already linked in the lead
 Done U+003F? 08:29, 28 September 2012 (UTC)[reply]
  • the references could use a bit of tidying; this is beyond GA-level requirements, so feel free to ignore (although I may clean them up myself in that case!)
  • journal titles should be in title case consistently (and please fix the ALL CAPS in Cheltsov 2001)
 Done U+003F? 10:01, 29 September 2012 (UTC)[reply]
  • similarly, journal article titles should be consistently in either title or sentence case (the latter is more usual)
 Done U+003F? 10:01, 29 September 2012 (UTC)[reply]
  • 3.0-A -> 3.0-Å
 Done U+003F? 08:29, 28 September 2012 (UTC)[reply]
  • "Correct folding of circularly permuted variants of a beta alpha barrel enzyme in vivo" -> "... of a βα barrel ..."
 Done U+003F? 08:29, 28 September 2012 (UTC)[reply]
  • Qian 2005 needs the species name italicized
 Done U+003F? 08:29, 28 September 2012 (UTC)[reply]
  • Beernink et al. 2001, change alpha to α
 Done U+003F?

Thanks again. I've had a first pass at dealing with your comments and suggestions. Let me know what you think. U+003F? 17:56, 3 October 2012 (UTC)[reply]

  • I've had a look at the recent literature in this topic and am confident that the article meets the criteria 3a ("addresses the main aspects of the topic") and 3b ("stays focused on the topic without going into unnecessary detail"). I've also verified several of the statements in the article and think the article complies with criteria 2a, b, and c. The images all have Wikipedia-compatible licenses. I'll be happy to promote to GA once the last issue with the lead is addressed. Sasata (talk) 07:26, 5 October 2012 (UTC)[reply]
  • Ok, all of my concerns have been resolved satisfactorily, and I am confident that the article meets the GA criteria. Good working with you, and I hope to see more of these computational biology topic pages here at GAN! Sasata (talk) 03:09, 6 October 2012 (UTC)[reply]
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