User talk:Andorsch

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We're so glad you're here! Paul (talk) 23:34, 26 February 2011 (UTC)

Thanks for the welcome, Paul! It is a small world and funny that we meet on wikipedia again :-) Andreas aka --Andorsch (talk) 08:07, 27 February 2011 (UTC)

It is indeed a small world. Google tells me you're Andreas Prlic. I hope all is going well in sunny California. I look forward to working with you in Wiki world. :-) --Paul (talk) 09:00, 27 February 2011 (UTC)

Your submission at Articles for creation

Philip Bourne, which you submitted to Articles for creation, has been created.

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Alpha Quadrant ^talk 19:21, 27 February 2011 (UTC)

A discussion you might want to get involved with

Hi Andreas, User:Alexbateman has started a thread discussing the PDB that you might want to get involved with: Wikipedia_talk:WikiProject_Molecular_and_Cellular_Biology#PDB_referrals_from_Wikipedia. Also a good chance to make yourself known to the MCB crowd.--Paul (talk) 14:11, 28 February 2011 (UTC)

Further to Alex's comment, some actual numbers might be useful.--Paul (talk) 14:12, 28 February 2011 (UTC)

Thanks, Paul, what numbers are you interested in? Not sure if I can post them in public, probably better to chat offline about this. --Andorsch (talk) 15:24, 1 March 2011 (UTC)

Probably doesn't matter. The number of visits from Wikipedia was what I was referring to. The main point of the discussion doesn't seem to be this however. BTW, you can sign your comments by hitting the little signature/pencil icon above the edit box or with four tildes. --Paul (talk) 16:33, 1 March 2011 (UTC)

More PDB query questions

Hi Andreas. I have two additional PDB query questions. The first question, is the use of "smartSubquery.do?smartSearchSubtype" documented anywhere? I tried googling, but I have not found anything. The second question is it possible to search for all the PDB structures that that contain a certain Pfam domain? This would provide an elegant solution to the pfam infobox controversy. A single link to the PDB (and an analogous link to PBDsum) could be added to the pfam infobox and as an added benefit, this link would not have to be maintained. Boghog (talk) 15:40, 5 March 2011 (UTC)

To give you an idea what I hand in mind, a created a test {{PFAM PDB}} template based on this pdb to pfam accession number list. When given a pfam accession number, this template will return a link to the RCSB PDB returning all the PDB structures that contain that pfam domain. For example {{PFAM PDB|PF00104}} will return the link "{{PFAM PDB|PF00104}}" to all the PDB structures containing nuclear receptor ligand binding domains. Given the enormous size of this template and the need to maintain it, I don't think it will be practical to use. Ideally I would like a way to directly query the PDB with the Pfam accession number and return the same type of list. Is this possible? Boghog (talk) 21:32, 5 March 2011 (UTC)

One additional note. Pfam searches of the PDBe are possible, for example PDBe:PF00104 or PDBe:PF00104. I have not however been able to figure out how to do this with PDBsum. Boghog (talk) 22:33, 5 March 2011 (UTC)

Sorry to butt in here Andreas and Boghog, but you might be better off doing this via Pfam rather than PDB, EBI, ... For each release Pfam provides a mapping between their families and PDB. Web access can be done via the website by family or by PDB ID. If you prefer flatfiles than you could probably find something on the ftp site.--Paul (talk) 23:26, 5 March 2011 (UTC)

Thanks Paul. The Pfam "family/piwi#tabview" link (e.g., Pfam:PF00104) is certainly useful and I would support adding it to the Pfam infobox. Boghog (talk) 06:39, 6 March 2011 (UTC)

I have made a mockup of how the new structure links might look in the pfam infobox here. Hopefully this would address everyone's concerns. Boghog (talk) 09:07, 6 March 2011 (UTC)

Great! I'm sure that'll make the Pfammers happy.--Paul (talk) 10:09, 6 March 2011 (UTC)

I prefer the one on the right. The long list of PDB IDs is not very useful. None of the other links appear to do a good job of serving up so many IDs either. But that's their problem, not WPs.--Paul (talk) 18:49, 6 March 2011 (UTC)

PF00104 is an extreme example with a lot of PDB structures associated with it and I would agree that a long list of the external PDB links in this pfam box is not very informative. I think each of the links on the left has their own advantages and disadvantages. The Pfam link of course gives detailed information on the chains and residues that make up the domain and the AstexViewer is cool. The RCSB PDB link has a drill down tool to select subsets. In this particular example, SCOP hits tab I think is especially informative. Boghog (talk) 19:47, 6 March 2011 (UTC)

You guys are fast! (and probably a few time zones ahead, well I know Paul is) ;-) The modified template is great. here my 0.02$:

1. Great to also include PDBe as a reference. They should be treated equally.
2. Would it make any sense to have human readable names, rather than database IDs? e.g. Hormone_recep instead of PF00104 ?
3. If I want to search for Pfam hits in PDB I use Hmmer3 at http://hmmer.janelia.org/search
4. RCSB PDB currently does not calculate weekly Pfam annotations, but we are loading the data weekly from Pfam and PDBe/the SIFTS project. If you think it is useful I can set up an entry point that allows to access via Pfam ID.
5. Another action point for me: make the documentation of links more transparent.
6. Tiny detail, in the template, can you enable the link across both words RCSB PDB, not only the last 3 characters? I think would look cleaner..

Thanks again Paul and Boghog for your help and constructive responses, --Andreas (talk) 19:43, 6 March 2011 (UTC)

Concerning point #6, the {{PFAM PDB}} template really needs to be replaced. It so big, I cannot even edit it before the Wikipedia server times out. Ideally I would like a direct pfam query link to the RCSB PDB analogous to the one that I am using to query PDBe. Is this possible? I guess this is what you are referring to in point #4. If so, I would appreciate if you would set this up. Thanks. Boghog (talk) 19:55, 6 March 2011 (UTC)

I added your feature request to our bug and feature tracking system. I'll let you know when the URL for this becomes available.--Andreas (talk) 20:10, 6 March 2011 (UTC)

Re: 0. I will be even more ahead soon, I'm moving to NZ in April. :-) Re: 3, is that a question? Yes, use HMMER3. You can get all the Pfam HMM libraries from the ftp site.--Paul (talk) 21:31, 6 March 2011 (UTC)

Yes, I have heard that you are moving to Christchurch. All the best for this big move! 3) is not a question but a statement  ;-) There is also the web service API I am interested in ... --Andreas (talk) 01:13, 7 March 2011 (UTC)

Thanks Andreas for adding my feature request to your request tracking system. I have made a slight modification to the {{Infobox protein family/sandbox}} template transcluding a new {{Pfam2pdb}} template so that the links to RCSB PDB are clearer (a test case can be seen here). Likewise I wish you every success in your move Paul. With the three of us spread across the globe, we can keep this conversion going 24/7;-) Boghog (talk) 06:57, 7 March 2011 (UTC)

Thanks for the wishes. I'll be based in Dunedin at first, until Christchurch is back up and running. The template looks very good, once the PDBSum placeholder is filled it should be good to go, right? --Paul (talk) 07:47, 7 March 2011 (UTC)

I have a temporary solution for the PDBsum links (see the updated testcases) that I think is good to go. In parallel, I will contact the PDBsum developers/maintainers to see if we can get a Pfam query link working that would provide a better long term solution. Boghog (talk) 08:49, 8 March 2011 (UTC)

That looks like a very good solution. At least until a Pfam ID hook can be added to PDBSum. The maintainers are on campus at the EBI. I/Alex could have a word also if you like. --Paul (talk) 12:23, 8 March 2011 (UTC)

I brought up the issue with Roman Laskowski who runs PDBsum. I think it is possible, I've asked when something like that could be made ready. Alexbateman (talk) 13:59, 8 March 2011 (UTC)

Alex, thanks for contacting Roman Laskowski. As you already know him, you are likely to be much more persuasive than I. There are a few house keeping chores that I need to do in parallel with putting the updated Pfam template into production that will take more time to complete than I have right now. But I should have time this weekend to finish the job. Again, thanks to both of you for your help. You have both been great! Cheers. Boghog (talk) 18:08, 8 March 2011 (UTC)

Quick update, I sent offline a link to Boghog where he can test the upcoming new URL that allows access to RCSB via Pfam id. We will also release a new advanced search for Pfam ids at the same time. --Andreas (talk) 18:36, 8 March 2011 (UTC)

We should discuss it at the talk page of template, rather than on our personal talk pages. I just came back from a business trip and made a few comments there [1].Hodja Nasreddin (talk) 02:49, 10 March 2011 (UTC)

 Done The new version of the {{Infobox protein family}} has now been put into production (diff). I made a new {{Pfam2PDBsum}} that is transcluded into the infobox and removed completely the PDB parameter (all external PDB links are now derived from the Pfam parameter and the PDB parameter has been deprecated). As soon as pfam query links to the RCSB PDB and PDBsum databases are available, these can replace the {{Pfam2pdb}} and {{Pfam2PDBsum}} templates respectively. Cheers. Boghog (talk) 16:26, 12 March 2011 (UTC)

File permission problem with File:Phil E Bourne.jpg

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WikiProject Computational Biology

Hi,

Thanks for signing up to WikiProject Computational Biology. There is a growing list of tasks that you can help out with if you have a few free moments. See the discussion page. Alexbateman (talk) 09:13, 9 June 2011 (UTC)

Thanks, Alex, I'll take a look! --Andreas (talk) 19:45, 9 June 2011 (UTC)

Requesting review of an article

Hey Andorsch, I saw that you're a member of the Computational Biology WikiProject group thing, that you're very interested in proteins, and that you appear very knowledgeable. Over the last several months I have put significant effort into improving the Folding@home article, which is about a powerful worldwide distributed-computing project that simulates protein folding and other molecular dynamics. My goal is to get it to a Good Article by January if I can. I'm aware that it's probably not there yet, but I'm looking for some knowledgeable reviewers to read over the article and let me know what changes I should make, or there's some scientific information that ought to be included. I'm a sophomore studying Computer Science at Utah State University, so one of the issues I've been having lately is trying to correctly interpret complex and technical scientific journals about protein folding. This is a necessary job because Folding@home has generated significant results in that area, and the article needs say why the project is significant in the first place. In short, I'm hoping that your expertise could confirm my writing, as well as offer any suggestions on how I can further improve the article in general. I'm quite enthusiastic about the project, and I'd be happy to make the changes you suggest if you don't feel you have the time to make them yourself. Thanks for any help you can provide. Jessemv (talk) 00:20, 23 October 2011 (UTC)

Hi Jessemv, what time frame are you expecting for this? Next two weeks are already quite busy for me, but I could take a look at some point after that. I have never reviewed a page on wikipedia so far. This will be a learning process how to do wiki reviews for me as well. --Andreas (talk) 04:46, 23 October 2011 (UTC)

Oh its not a big deal. Whenever you can really. It's completely understandable that you have really important things to do, and by no means is this a high priority. So whenever you finish your business in two weeks would be fine. Reviewing a page at this point I believe should be easy. It should basically consist of a read-through, and then making a section on the talk page outlining any issues you find. What I'm just looking for now is a few people to make sure I have things right, and offer suggestions as to what I should change/improve to get the article closer to Good Article criteria. Once those people run out of ideas, then the article should be looking pretty good and I'll open the peer review up as much as I can. So basically what I'm envisioning is 1) a few knowledgeable people help confirm that the facts are straight and the article's organization is in order, 2) larger peer review begins for further polish and suggestions, 3) the article is nominated to be a Good Article, where it should be only a few minor edits away from passing, 4) it becomes a Good Article and I rest and celebrate. That's what I'm thinking. Jessemv (talk) 06:00, 23 October 2011 (UTC)

DYK for Circular permutation in proteins

The Bushranger _{One ping only} 08:41, 17 April 2012 (UTC)