Knowledge (XXG)

Template talk:PDB

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1227:. The original scientific publication can be considered as both a primary source (since it was written by the researchers who collected and interpreted the data) and as a secondary source (since it was peer reviewed by two anonymous referees and the journal editor). The RCSB-PDB can also be considered as both a primary source (since the coordinates, structure factors, and experimental details are stored there) as well as a secondary source (since the deposited structures must undergo a quality check before they are released). PBDSum provides no additional quality checks above and beyond what the wwPDB has provided, therefore PDBSum could at most be considered a tertiary source. Adding additional links helps to interpret the experimental structure, but does nothing to verify it (e.g., does the structure adequate fit the electron density, are there any severe geometrical outliers, etc.). 1334:
data like structure factors is not. Furthermore these experimental details are more throughly reported in the "Materials and Methods Report" tab in the RCSB-PDB. The RCSB-PDB also provides much more extensive searching and reporting capabilities including the ability to include experimental details as optional search parameters. This is important for example in locating the best structure(s) (highest resolution, crystallization pH close to physiological) to include in links from Knowledge (XXG). One last point: there is a link from the RCSB-PDB structure entry back to the corresponding PDBSum entry under the external links section. So for interpretation of the structure, they are available from the RCSB-PDB by clicking back to the PDBSum. "So, there are no important differences here." Cheers.
884:. What is being verified here? It is the experimentally determined structure. Many funding agencies and scientific journals require that the coordinates of structures be deposited in the PDB. The PDB has the task of insuring that these structures conform to certain quality standards, are properly documented, are assign a unique accession code (which by the way, is universally used by derivative databases including the PDBSum), and are made freely available to everyone. In addition, the PDB has the most complete on-line information about the experimental conditions under which the data was collected and this information is important in verification and in the interpretation of the structures. Furthermore the PDB is now requiring that 1279:. That is a misinterpretation of what I wrote above. I think it is important to distinguish between verification of the experimental structure which RCSB-PDB provides and interpretation of the structure which both the RCSB-PDB and PDBSum provide. I would agree that the PDBSum provides more links and therefore is better for interpreting the structure within a biological context, but the RCSB-PDB provides the essential minimum (PubMed citation + PFAM, SCOP and CATH). What the RCSB-PDB provides which the PDBSum does not is the hard data and experimental details which is essential for judging the quality and relevance of the structure. 1493:
this by a single click from the PDBsum link. However from an RCSB-PDB links, I should go first to "External links" (I have learned this from you only 30 minutes ago), then find PDBsum link at the bottom of a page, and so on. Only a WP reader who is more advanced than me (perhaps you) will ever do that. So, I still believe that PDBsum link is better. But let's simply keep all templates as they are right now, since we can not agree on that. Dan changed it to RCSB-PDB, so consider that your position prevailed. I do not care about WP users so much to continue this discussion. Thanks. No any hard feelings about that.
668:. It seems totally reasonable to format links differently for 'large scale' use in boxes (as argued above). And I can almost see the point of adding a link to the PDB also (although I still want to check through some articles to see if this is really necessary). However, with regard to link destination, I think it is confusing and wrong to have links pointing to different destinations. I think we should reach a consensus and harmonize the link destination (changing many thousands of articles if necessary - isn't that the whole point of templates?). -- 980:. Specialists (like you or me) will never download protein structures by reaching them through WP articles, and non-specialists do not need to download anything. Remember that WP is designed for general public, high school students, etc. A common wikipedia reader only needs is a good portal to other internet resources and good graphics that shows various features of the proteins, such as subunit structure, secondary structure, ligands etc. That is where PDBsum much superior. 1651: 864:. The PDB does in fact provide text information. On the left hand side of any structure page in the PDB is an expandable list of "Download files" which includes the header text, full text (header + coordinates), and the coordinate data in a number of formats (xml, mmCIF, etc.). As far as I can see, PDBSum only provides the header information and not the coordinates. If you want the coordinates in PDBSum, you must follow the links back to the PDB. 1312:". What that suppose to mean? Both databases give an easy link to the same PDB file header which describes experimental conditions (it looks a little bit nicer in the PDBsum); both databases give the same R-factor, resolution, R-free, and so on (it seems that PDBsum is missing only the crystallographic group of symmetry). So, all experimental details are practically the same (there is a database of protein crystallization conditions 1027:. You might be surprised. Occasionally I might run into an WP protein article that interests me and I will want to down load the structure, if for no other reason than to produce a PyMol figure to add back to the article. Of course, I have a half dozen other ways to download the coordinates, but if I have a direct link right there right in front of me without having to double click through the PDBSum site, it is more convenient. 786:
the first site that will make available new structures and the first site that will publish corrections. The primary purpose of links in WP is verification and secondary purpose is additional education. WP articles should to the greatest extent possible be self explanatory and not rely on external links for understanding. Hence IMHO, reliability and timeliness should take precedence over adding additional understanding. Cheers.
2264: 2130: 1689: 1597: 1516:. That is to say, when the page writes the content from the template, it applies the markup in the wrong order. It takes the link text and makes a link before it looks at the outer brackets. I don't know what would be causing this, but it seems to be a rather technical error, since there is nothing obviously wrong with how the template is written. - 2345: 2223: 1744: 888:
be included in any structure that is deposited in the PDB. While it is highly unlikely that a Knowledge (XXG) reader would check a structure using the structure factors, these factors provide the most rigorous level of verifiability that the data for the structure was collected and interpreted in an
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What kind of link is better for "PDB" is an open question. From WP perspective, it does not matter if a site is "official" or not. A lot of "official sites" are spam. We have no obligations to PDB and we are not affiliated with PDB in any way. The links must be "educational", convenient for a reader,
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That is easy to say, and I follow the argument above, but I would like to revisit this discussion. How / where are the above link options compared and contrasted? How do we keep that comparison up to date? Despite what you put above about the concept of an 'official' site, which I think is generally
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Now I see... I should go from a RCSB-PDB entry (say 1gzm) to "External links" (this link does not work with mozilla on my SGI computer!), then find PDBsum at the bottom of a very long page, and click PDBsum. No WP reader will ever do that. In PDBsum however, all links to other databases (and a lot
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Point #1 (verifiability) takes precedence over point # 3 (adding additional understanding) and you have not responded to that issue. While the crystallographic group symmetry and crystallization conditions are included in the header information (and therefore accessible from both databases), other
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the corresponding paper is published in the scientific literature. In addition, the paper invariably references the coordinates deposited in the PDB. Hence for all practical purposes, the PDB becomes an inseparable part of the paper. Therefore to provide a complete citation, one not only needs to
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PDBsum provides quick link to standard PDB (and many other resources), whereas standard PDB does not provides link to PDBsum. So, the PDB is only one click away of PDBsum, but not vice versa. Finally let's not discuss "verifiability" issues to save some time. You would probably agree that PDB is no
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Good job! I think the question by Dan about the best destination is reasonable. As I noted above, there are huge advantages from educational/WP perspective to use PDBsum whenever possible, unless someone can explain why "official" PDB link is better - I think only crystallographic group of symmetry
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much. The problem is: a reader goes to the standard PDB link, and he does not know anything about the existence of PDBsum and other protein structure databases. However if he follows PDBsum link (as I suggest), he will see the links to RCSB-PDB and 21 other protein structure/sequence databases. As
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Two points in favor of PDB. First is up time. As I write this, the PDB site is up and PDBsum is down. The PDB is mirrored, and to the best of my knowledge, PDBsum is not. The second is timeliness. When I want to download coordinates of a structure, I go to the primary source, the PDB. This is
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No. Only 3D coordinates of proteins come from RSCB PDB. In addition to 3D coordinates, the derivative databases (and partly RSCB PDB) include a lot of other data: amino acid sequences, ligands, chemical reactions catalyzed by enzymes, secondary structure, automatically generated pictures of ligand
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a number of additional graphic representations (!) from the PDBsum link, but he will see only 3 immediate links to other databases from a PDB entry and nothing else. To clarify, let's consider a simple practical example. I want to see a Uniprot annotation of subunit C from PDB file 2axt. I can do
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I have used the PDB for close to 20 years as a source of coordinates for structure based drug design. The coordinates can be downloaded from the PDB and not from the PDBSum. In other words, the PDBSum lacks essential data that is required for my work. I think the confusion here is that different
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And I strongly support Andrew. There is a reason for doing this. The PDB2 template is currently used in the ProteinBox template (many thousands of articles). By creating the additional PDB2 template, Andrew makes sure that any changes of "main" PDB template (like you did) will not affect his work
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source of the data (note the lack of inverted commas around that last use of the word official). Is it possible to make a page listing the major PDB derived databases with comparisons according to key features? It seems like that is what we need to begin to address this question, but I don't know
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Verifiability is the single most important issue, and on this point, there is no contest. As the original definitive source of the coordinates, structure factors, experimental details, the PDB is a far superior to PDBsum. The only verifiability that the PDBsum has is its links to the original
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The entire EBI site is down today, not only PDBsum. That can happen anywhere. Right, there are no mirrors except PDB iself, which can be easily accessed (if PDB is down, you do not get an instant access either with links from WP). Pleas note that PDB links do not verify anything, because this
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with ProteinBox template. Same thing was done by WillowW (enzyme articles) and by me (PfamBox). This also creates an extra flexibility. If anyone of us decides to switch to MSD instead of standard PDB in all higher-level templates, one can easily do so without affecting anything else.
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users have different requirements. From a bioinformatics perspective, the PDBSum has some advantages. For structural biology, PDBSum lacks the most basic data (the coordinates). In short, I think PDBSum is a nice complement to but was never intended to replace the PDB. Cheers.
1245:. Yes, this is true. However, RCSB-PDB is only one click away of PDBsum (the link is there). Moreover, one would normally use searches in RCSB-PDB or more reliable scientific databases (such as SMART) rather than wikipedia to identify and download the PDB files of interest. 1133:. Yes, this is true. However, RCSB-PDB is only one click away of PDBsum (the link is there). Moreover, one would normally use searches in RCSB-PDB or more reliable scientific databases (such as SMART) rather than wikipedia to identify and download the PDB files of interest. 1184:
I could continue this list, but the overall picture is clear. Actually, this is a perfect example why a secondary source (PDBsum) is better than a primary source for WP. It provides references/links to numerous different primary sources, whereas the primary source does
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I don't think it is incorrect to do so. Where does structural data come from if not from the PDB? People add links to that data and pull in information from other resources to supplement that data, but ultimately it all comes from (stems from) the RSCB PDB. Dosn't it?
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database does not provide any information as text, except PDB headers (after a couple of extra clicks). This is contary to PDBsum which provides abstract of key articles, or UniProt which provides annotations. Therefore, PDBsum, or UniProt can be used for
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is preferable since it clearly indicates an external link. While I agree we should standardize and consolidate when appropriate, I don't think we need to be too aggressive about this if it means sacrificing these subtle (but important) differences.
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OK, I'll have a look and see what there is to see. I am slightly worried that you favour one site because you are more familiar with that site, but I'll have a look. I have also found many bugs on the PDB site, so I know where you are coming from.
876:. I have not done an exhaustive comparison, but it appears that the PDB provides many of the same links that are found in the PDBSum. The links in PDBSum may be organized better, but they are for the most part also included in the PDB. 1915:​), in which case the extra space at the end of the template looks odd before the closing bracket. Currently it looks to me as though the two requirements (use in image caption vs use in brackets) are mutually exclusive. Any ideas? 870:. The PDB also provides the abstract as well as a link to the corresponding PubMed citaiton. In addition, the PDB provides a direct link to the relevant UniProt page under the "Sequence Details" tab on every structure page. 2077:
I can't imagine anyone needing to reference a list of more than 9 so that seems good. What do you think of the slightly more compact formatting and plainlinks style that I edited into the sandbox (similar format to
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is better in PDB than in PDBsum. On the other hand, let's respect opinions of people who are using PDB links in the more complicated templates. If AndrewGNF wants to use "official" PDB in ProteinBox, so be it.
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and that seems to have solved the problem. I am not sure what caused the problem in the first place or why adding a space fixes the problem. In any case, the problem in this article seems to now be resolved.
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of that can be found in the "standard" PDB. I could continue and make this list much longer. Just look yourself and trace the links provided in PDB and PDBsum. "Standard PDB" is a very poor job compare to
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A common wikipedia reader only needs is a good portal to other internet resources and good graphics that shows various features of the proteins, such as subunit structure, secondary structure, ligands etc
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Boghog2, did you look and compared both sites? Did you ever use yourself these databases in your work? The difference between PDB and PDBsum is obvious and significant. Otherwise, I would not argue here.
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purposes, whereas PDB is not. The PDB/PDBsum links are mostly useful to provide some graphic information about proteins and to serve as "gates" to other internet resources, and that is where PDBsum much
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and would object to its disappearance. This template is well suited to the PBB infobox, in which the external link icon would really take up a substantial amount of space. (For example, the list for
1372:. And in that regard the PDBsum link provides much more information and options. One does not need any search facilities, since the proper link has been already provided in an WP article. 1488:
No, SGI has nothing to do with it. Everything boils down to a very simple thing (see Argument#3, "Take two"). A WP reader will see easy links to 22 protein structure/sequence databases
1394:, 3D coordinates and structure factors) that are not stored in PDBSum database. To the extent that the PDBSum tertiary source links back to the primary/secondary source of the data ( 874:
The PDB/PDBsum links are mostly useful to provide some graphic information about proteins and to serve as "gates" to other internet resources, and that is where PDBsum much superior
1398:, RCSB-PDB), both databases contain the same data. But why not link directly to the primary/secondary source of the data, the RCSB-PDB rather than a tertiary source like PDBSum? 238:
binding pockets, modeled protein movements or arrangements of proteins in membranes, and so on. Many of these data can be found only in derivative databases, but not in RSCB PDB.
1315:, but we are not talking about it). As about "hard data" - they are available by clicking "RSCB" or "MDB" links in the PDBsum menu. So, there are no important differences here. 1033:
You are making assumptions about what a reader might be interested in which might not apply in all cases. Furthermore, the PDB provides much the same information as PDBSum.
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better for verification purposes than PDBsum, and that link to PDB is not good for verification purposes (one should refer to publications in books and journals).
1168:, its topology diagram, amino acid sequence and regular secondary structure (please click further to "sequence" motifs, and so on). RCSB-PDB has nothing of that. 1310:
RCSB-PDB provides which the PDBSum does not is the hard data and experimental details which is essential for judging the quality and relevance of the structure
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If this is not acceptable for some reason, we can instead add several off site links per PDB code, for example (taken from the list of links maintained at
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As a derivative database, it is natural that PDBsum would link to PDB. I agree that it would be nice if the PDB provided a link back to the PDBsum.
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P.S. Of course I am not telling such stupid thing that PDBsum was intended to replace the PDB! We only discuss which link is better for WP purposes.
2051:​ Is 9 parameters sufficient? I can add support for additional parameters, but the template coding is a bit tedious. One probably could use 2291:
The Zero-width space solution has been implemented in the sandbox. Admins, if you agree, with the proposed change, could you implement it?
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and nice diagram with topology, amino acid sequence and regular secondary structure; please click further to "sequence" motifs, and so on
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The original PDB link (let's call it RCSB-PDB) is better because this is a primary deposition site of data, a kind of "primary source".
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The original PDB link (let's call it RCSB-PDB) is better because this is a primary deposition site of data, a kind of "primary source".
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PS: I have fond memories of SGI. I hope I don't start any OS religious wars, but in some ways, I still prefer the IRIX GUI to Linux.
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argument that RCSB-PDB has a better search facility. However this is irrelevant. Templates we are talking about make a reference to
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PDBsum provides seven times more links than RCSB-PDB and a lot of additional graphical and other capabilities that RCSB-PDB does not
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Please compare "2axt" (as a random example) in PDB and PDBsum. The interface by PDBsum provides, among other things, the following:
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I think this is the wrong link for PDB codes, as the above database is just one example of many derived database based on the PDB.
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I agree that the plain links is a good idea, but the list is a bit too compressed for my taste, so I have restored the spaces.
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PDBsum provides quick link to standard PDB (and many other resources), whereas standard PDB does not provides link to PDBsum (
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I agree too. However, I don't think the story ends here. Lets be clear, there are two arguments to discuss here, one is link
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Changed protection, but I'll let you do the honors, since I'm not brave enough to edit a popular template from a tablet :)
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I've though of a possible solution that solves the problem whilst avoiding inserting extra spaces about the place: Use the
549:(or vice-verse). It looks like the difference is minimal, the question is related to the general style of external links. 1429:. But if they follow PDBsum link, they will see a lot of them. If they follow RCSB-PDB, they will see only three of them. 155:
is better than "official site". PDB has enormous resources and does very poor job, probably due to management problems.
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5. PDBsum includes pictures with secondary structure and their topologies generated by PROMOTIF. RCSB-PDB has nothing.
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Here is an example call to each of the five different PDB templates that I have found in common usage, namely 1)
1769: 1734: 1308:? Good. Then we can agree at least on something. But you tell that I am missing the following point of yours: " 1177:
6. PDBsum has pictures with chemical reactions for enzymes and links to enzyme databases. PDB-RCSB has nothing.
322: 228: 1551: 1271:. No, that is not the case. This is main point and should be explained in detail (see 2axt as an example): 1147:. No, that is not the case. This is main point and should be explained in detail (see 2axt as an example): 2177: 2232: 2207: 1753: 1161:
2. PDBsum usually includes an Abstract of key crystallography paper with key Figures. RCSB-PDB does not.
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Specialists (like you or me) will never download protein structures by reaching them through WP articles
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Sorry, but your point #1 (verifiability) is groundless because we are talking about different links to
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The current usage is ... 212, 903, 4, 2986, and 166 times, respectively (as of a couple of days ago).
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http://en.wikipedia.org/search/?title=Human_leukocyte_antigen&diff=556740430&oldid=553201860
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optimal way and the PDB to my knowledge in general the only place where this data can be obtained.
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better interface than the official PDB (I can easily explain why). We discussed this question with
1750:. The /doc subpage isn't protected though - next time you can just do it yourself. Best regards — 1494: 1445: 1430: 1373: 1316: 1186: 1004: 990: 930: 823: 748: 647: 336: 302: 239: 205: 156: 75: 171:
reasonable, somehow when it comes to data providers I think we have an obligation to link to the
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PDB links do not verify anything, because this database does not provide any information as text
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I am going to update the template to point at the appropriate page of the official PDB website;
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to provide support for unlimited number of parameters, but this is beyond my coding knowledge.
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and add value to WP articles. In that regards PDBsum is the way to go, because it provides a
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The sandbox has been modified to allow up to 9 parameters: {{PDB/sandbox|3BSE|1OBB|3TRA}} →
1925: 1723: 1658: 1573: 1541: 885: 2181: 2180:). I would appreciate if the main template were synched with the sandbox. Better yet, if 2052: 1512:
This template does not render correctly. For example, I see the following in an article:
1039:. I agree that PDBSum has a nice layout, but I think you are overstating the superiority. 582:. i.e. is that call to the PDB article really needed on the pages that use this template. 284:
Pictures with secondary structures, including beta-sheet topologies produced by PROMOTIF;
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you can see from the discssion above, many people (like Dan) do not know much about the
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Link to each subunit (row at the left) - click there and you will see the picture of an
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I think such a suite of links in addition to the official link could be quiet nice. --
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PDBsum which provides abstract of key articles, or UniProt which provides annotations
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I just added a space between the pdb template and the closing image bracket in this
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You would probably agree that PDB is no better for verification purposes than PDBsum
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and the result (wrong; link broken; extra ] is shown after image as wikitext) is
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http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1xyz
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looks like a good solution so I have implemented it. Thanks for the suggestion!
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3. PDBsum has link to each subunit (row at the left) - with the picture of an
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cite the scientific literature, but also the coordinates deposited in the PDB.
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literature plus the PDB. Please note that structures often appear in the PDB
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So the whole argument now boils down to whose cross link is most accessible?
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List of ligands - click at any ligand - and you will see something like that
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rights were added to this template, I can make the changes myself. Thanks.
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Hello. There is a problem with usage PDB template in images. Here the diff:
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4. PDBsum has diagrams of ligand binding pockets. PDB-RCSB has none of that.
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What user would prefer link to PDB rather than to PDBsum from WP articles?
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What user would prefer link to PDB rather than to PDBsum from WP articles?
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Yes, the PDB database is more convenient for downloading the coordinates.
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The two requests immediately above have been implemented in the sandbox:
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Where did you see a link from PDB entries to PDBsum? I do not see any.
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but the PDB does provide links to many of the same third party sources
441: 433: 416: 204:, just like PDB itself. Calling them "PDB derived" would be incorrect. 101:
PDB templates right now: "PDB2" ("official site"), in ProteinBox (see
1881: 1239:. RCSB-PDB is better for downloading the 3D coordinates of proteins. 1127:. RCSB-PDB is better for downloading the 3D coordinates of proteins. 2368: 2337: 2320: 2295: 2246: 2215: 2193: 2112: 2094: 2064: 2019: 1951: 1919: 1856: 1771: 1760: 1736: 1673: 1643: 1577: 1558: 1545: 1520: 1502: 1469: 1453: 1438: 1407: 1381: 1343: 1324: 1298: 1194: 1089: 1055:). So, the PDB is only one click away of PDBsum, but not vice versa. 1012: 998: 953: 938: 898: 831: 795: 780: 756: 737: 702: 693:
and transcluded it from the various PDB templates above. thoughts?
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Request disabled pending discussion of the best solution. — Martin
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So, you do not dispute my last and the only important argument 3:
1865:] (no space between "}}" and "]]" which now renders correctly as: 529:
The question remains as to whether it does any harm to convert
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Does anyone know of any issues that would stop it working?
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http://www.rcsb.org/pdb/explore/explore.do?structureId=1XYZ
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Apologies for being difficult, but I've just noticed that
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In the interest of keeping everything straight, I created
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It really does help when translating articles. Thanks :)
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Looks good. Lets move some of the other information from
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From the PBB perspective, I very much support the use of
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Certainly not a student, and not a specialist like me.
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Links to many other databases that are not linked to PDB
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Sorry, but I can not agree. There are two main points.
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Abstract of key crystallography paper with key Figures;
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Is it possible to add some spacing into the template?`
1265:. PDBsum has no significant advantages over RCSB-PDB. 1215:. No, we have to provide best "secondary" sources per 1141:. PDBsum has no significant advantages over RCSB-PDB. 1115:. No, we have to provide best "secondary" sources per 978:
But a wikipedia reader does not need these coordinates
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the same coordinates (3D structure) and the same data
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Which PDB link is better for wikipedia? Take three.
1680:Edit request from Jacopo Werther, 26 November 2012 1368:PDB file. So, the only important question is what 1253:. I would agree that this is not a critical issue. 1098:Which PDB link is better for wikipedia? Take two. 1801:When PDB template is used in image description: 1588:Edit request from MindZiper, 13 September 2011 1102:I guess Boghog2 made the following arguments. 290:Links to UniProt records (this is important); 287:Pictures with chemical reactions for enzymes; 8: 1971:({{PDB|3BSE}}, {{PDB2|1OBB}}, {{PDB2|3TRA}}) 761:I'm agnostic, so if you guys want to change 610:is already quite long -- imagine that using 858:The following points need to be clarified: 2305:, since he is familiar with this issue. -- 1444:of other options) are immediately vizible. 1420:If there was such link, I would not argue 178:Comparison of online PDB derived databases 105:), "PDB3" (PDBsum site) - in PfamBox (see 2162: 1765:Sorry, you are right! Thank you so much! 1061:Finally let's not discuss "verifiability" 620:.) However, I imagine for inline links, 2001:to make something that looks like (PDB 1550:That's the use that doesn't work. See 2176:And the changes work as expected (see 1158:other databases (PFAM, SCOP and CATH). 1075:. On this point, I strongly disagree. 585:Just a dump of my current thinking. -- 202:and a lot of other databases/resources 138:Please do explain why, I am curious.-- 192:I would recommend to create articles 7: 1716:Please add the missing interwikies: 1862:Error fixed in the sandbox version: 1807:it will be expanded as: (note ]]]) 1526:Try {{PDB|2G9H}} which renders as 1416:With regard to your last argument. 115:Category:Enzymes of known structure 21:Currently this template points to; 2169: 1037:That is where PDBsum much superior 732:... but ... well... lets try... -- 14: 1552:Human_leukocyte_antigen#Functions 1045:Oh, I don't know, me perhaps? ;-) 771:to PDBsum, I have no objection. 353:Comparing different PDB templates 176:where such a page should live... 2343: 2262: 2221: 2128: 1905:is often used in brackets e.g. ( 1742: 1687: 1649: 1595: 1719:] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] 1952:06:22, 16 September 2015 (UTC) 1674:14:49, 13 September 2011 (UTC) 1644:05:22, 13 September 2011 (UTC) 200:. Structure databases use PDB 1: 1772:14:37, 26 November 2012 (UTC) 1761:11:17, 26 November 2012 (UTC) 1737:08:50, 26 November 2012 (UTC) 728:. I am going to try to write 562:can be similarly merged onto 2369:03:56, 7 October 2015 (UTC) 2338:11:28, 6 October 2015 (UTC) 2321:16:00, 5 October 2015 (UTC) 2296:09:19, 5 October 2015 (UTC) 2285:to reactivate your request. 2273:has been answered. Set the 2151:to reactivate your request. 2139:has been answered. Set the 1710:to reactivate your request. 1698:has been answered. Set the 1618:to reactivate your request. 1606:has been answered. Set the 1427:Protein structure databases 1370:this specific link provides 730:Protein structure databases 552:The final question whether 335:So, did you look at PDBsum? 194:Protein structure databases 2387: 2027:Evolution and evolvability 1828:Correct result should be: 1503:21:37, 14 April 2008 (UTC) 1470:20:46, 14 April 2008 (UTC) 1454:16:28, 14 April 2008 (UTC) 1439:15:59, 14 April 2008 (UTC) 1408:20:46, 14 April 2008 (UTC) 1382:14:50, 14 April 2008 (UTC) 1344:06:45, 14 April 2008 (UTC) 1325:01:28, 14 April 2008 (UTC) 1299:21:20, 13 April 2008 (UTC) 1195:13:05, 13 April 2008 (UTC) 1090:19:03, 12 April 2008 (UTC) 1013:16:57, 12 April 2008 (UTC) 999:16:52, 12 April 2008 (UTC) 954:15:13, 12 April 2008 (UTC) 939:18:29, 11 April 2008 (UTC) 899:15:13, 12 April 2008 (UTC) 832:22:14, 10 April 2008 (UTC) 796:21:08, 10 April 2008 (UTC) 781:17:31, 10 April 2008 (UTC) 757:16:21, 10 April 2008 (UTC) 345:16:08, 10 April 2008 (UTC) 248:20:45, 12 April 2008 (UTC) 198:Protein sequence databases 131:and decided to use PDBsum. 2247:09:07, 28 June 2015 (UTC) 2216:08:58, 28 June 2015 (UTC) 2194:09:07, 27 June 2015 (UTC) 2113:06:45, 26 June 2015 (UTC) 2095:04:23, 26 June 2015 (UTC) 2065:04:04, 26 June 2015 (UTC) 2020:07:28, 7 April 2015 (UTC) 1920:04:10, 23 July 2015 (UTC) 1578:15:09, 15 July 2011 (UTC) 1559:14:21, 15 July 2011 (UTC) 1546:17:55, 11 July 2011 (UTC) 1521:15:48, 11 July 2011 (UTC) 738:20:54, 5 April 2008 (UTC) 703:20:15, 5 April 2008 (UTC) 674:20:54, 5 April 2008 (UTC) 656:16:58, 5 April 2008 (UTC) 641:01:22, 5 April 2008 (UTC) 608:Cyclin-dependent_kinase_2 591:15:50, 4 April 2008 (UTC) 327:15:31, 4 April 2008 (UTC) 311:03:53, 4 April 2008 (UTC) 233:15:31, 4 April 2008 (UTC) 214:03:53, 4 April 2008 (UTC) 186:20:36, 3 April 2008 (UTC) 165:15:53, 3 April 2008 (UTC) 144:20:36, 3 April 2008 (UTC) 92:09:59, 3 April 2008 (UTC) 1999:({{PDB|3BSE|1OBB|3TRA}}) 1857:15:29, 25 May 2013 (UTC) 1554:, first image caption. - 1390:RCSB-PDB includes data ( 1150:1. PDBsum has links to 2178:Template:PDB/testcases 1886: 1844: 1837:CORRECT: description, 516:can be converted into 492:can be converted into 1874: 1836: 1821: 1822:WRONG: description, 1366:a single and defined 664:, the other is link 103:Histone H2B type 1-C 2163:space after last ] 1624:Add the interwiki: 502:, and it certainly 1887: 1845: 1780:space after last ] 1166:individual subunit 723:PDB_template_usage 688:PDB_template_usage 273:individual subunit 2353:T.Shafee(Evo﹠Evo) 2336: 2293:T.Shafee(Evo﹠Evo) 2289: 2288: 2172:" feature request 2155: 2154: 2092:T.Shafee(Evo﹠Evo) 2017:T.Shafee(Evo﹠Evo) 1949:T.Shafee(Evo﹠Evo) 1917:T.Shafee(Evo﹠Evo) 1714: 1713: 1672: 1622: 1621: 886:structure factors 258:PDB versus PDBsum 2378: 2357:zero width space 2351: 2347: 2346: 2326: 2317: 2280: 2276: 2266: 2265: 2259: 2236: 2233:Opabinia regalis 2229: 2225: 2224: 2208:Opabinia regalis 2205: 2146: 2142: 2132: 2131: 2125: 2089: 2088: 2082: 2076: 2050: 2030: 2000: 1994: 1988: 1982: 1972: 1969:Currently I use 1941: 1937: 1936:ZERO WIDTH SPACE 1934: 1933: 1926:Zero-width space 1914: 1904: 1898: 1884: 1872: 1834: 1819: 1792: 1791: 1787: 1756: 1755:Mr. Stradivarius 1746: 1745: 1724:Template:PDB/doc 1705: 1701: 1691: 1690: 1684: 1662: 1659:Template:PDB/doc 1653: 1628:es:Plantilla:PDB 1613: 1609: 1599: 1598: 1592: 1535: 1217:WP:Verifiability 1117:WP:Verifiability 881:WP:Verifiability 819:WP:Verifiability 770: 764: 727: 721: 717: 711: 692: 686: 629: 623: 619: 613: 605: 599: 581: 575: 571: 565: 561: 555: 548: 542: 538: 532: 525: 519: 515: 509: 501: 495: 491: 485: 475: 469: 465: 459: 452: 444: 436: 419: 406: 400: 396: 390: 386: 380: 376: 370: 366: 360: 97:In fact we have 2386: 2385: 2381: 2380: 2379: 2377: 2376: 2375: 2344: 2342: 2311: 2278: 2274: 2263: 2257: 2230: 2222: 2220: 2199: 2182:template editor 2144: 2140: 2129: 2123: 2086: 2080: 2079: 2070: 2034: 2024: 1998: 1990: 1984: 1974: 1970: 1964: 1939: 1935: 1931: 1930: 1906: 1902: 1896: 1876: 1870: 1832: 1817: 1811: 1805: 1793: 1789: 1785: 1783: 1782: 1754: 1743: 1720: 1703: 1699: 1688: 1682: 1611: 1607: 1596: 1590: 1527: 1510: 1203: 1100: 1021:More comments: 768: 762: 725: 719: 715: 709: 690: 684: 627: 621: 617: 611: 603: 597: 579: 573: 569: 563: 559: 553: 546: 540: 536: 530: 523: 517: 513: 507: 499: 493: 489: 483: 473: 467: 463: 457: 448: 440: 428: 411: 404: 398: 394: 388: 384: 378: 374: 368: 364: 358: 355: 260: 38: 27: 19: 12: 11: 5: 2384: 2382: 2374: 2373: 2372: 2371: 2323: 2314: 2287: 2286: 2267: 2256: 2255:Requested edit 2253: 2252: 2251: 2250: 2249: 2174: 2173: 2166: 2153: 2152: 2133: 2122: 2121:Requested edit 2119: 2118: 2117: 2116: 2115: 2098: 2097: 1996: 1963: 1960: 1959: 1958: 1957: 1956: 1955: 1954: 1945: 1944: 1943: 1889: 1867: 1866: 1863: 1809: 1803: 1781: 1778: 1777: 1776: 1775: 1774: 1767:Jacopo Werther 1732:Jacopo Werther 1718: 1712: 1711: 1692: 1681: 1678: 1677: 1676: 1620: 1619: 1600: 1589: 1586: 1585: 1584: 1583: 1582: 1581: 1580: 1509: 1508:Rogue brackets 1506: 1486: 1485: 1484: 1483: 1482: 1481: 1480: 1479: 1478: 1477: 1476: 1475: 1474: 1473: 1414: 1413: 1412: 1411: 1410: 1349: 1348: 1347: 1346: 1328: 1327: 1287: 1286: 1285: 1284: 1283: 1282: 1281: 1280: 1277:Reply to Reply 1260: 1259: 1258: 1257: 1256: 1255: 1254: 1251:Reply to Reply 1234: 1233: 1232: 1231: 1230: 1229: 1228: 1225:Reply to Reply 1202: 1199: 1198: 1197: 1182: 1181: 1180: 1179: 1178: 1175: 1172: 1169: 1162: 1159: 1136: 1135: 1134: 1122: 1121: 1120: 1099: 1096: 1095: 1094: 1093: 1092: 1078: 1077: 1076: 1070: 1058: 1046: 1040: 1034: 1028: 1016: 1015: 1001: 969: 968: 967: 966: 965: 964: 963: 962: 961: 960: 959: 958: 957: 956: 916: 915: 914: 913: 912: 911: 910: 909: 908: 907: 906: 905: 904: 903: 902: 901: 877: 871: 865: 843: 842: 841: 840: 839: 838: 837: 836: 835: 834: 805: 804: 803: 802: 801: 800: 799: 798: 741: 740: 681: 680: 679: 678: 677: 676: 454: 453: 446: 438: 426: 421: 354: 351: 350: 349: 348: 347: 330: 329: 295: 294: 291: 288: 285: 282: 276: 269: 265: 264: 259: 256: 255: 254: 253: 252: 251: 250: 217: 216: 189: 188: 149: 148: 147: 146: 133: 132: 119: 118: 84: 83: 78: 73: 68: 63: 58: 53: 34: 23: 18: 15: 13: 10: 9: 6: 4: 3: 2: 2383: 2370: 2366: 2362: 2358: 2354: 2350: 2341: 2340: 2339: 2334: 2330: 2324: 2322: 2318: 2316: 2308: 2304: 2300: 2299: 2298: 2297: 2294: 2284: 2281:parameter to 2272: 2268: 2261: 2260: 2254: 2248: 2244: 2240: 2234: 2228: 2219: 2218: 2217: 2213: 2209: 2203: 2198: 2197: 2196: 2195: 2191: 2187: 2183: 2179: 2171: 2170:Multiple PDBs 2167: 2164: 2160: 2159: 2158: 2150: 2147:parameter to 2138: 2134: 2127: 2126: 2120: 2114: 2110: 2106: 2102: 2101: 2100: 2099: 2096: 2093: 2085: 2074: 2069: 2068: 2067: 2066: 2062: 2058: 2054: 2049: 2045: 2041: 2037: 2031: 2028: 2022: 2021: 2018: 2014: 2012: 2008: 2004: 1993: 1987: 1981: 1977: 1967: 1962:Multiple PDBs 1961: 1953: 1950: 1946: 1929: 1928: 1927: 1923: 1922: 1921: 1918: 1913: 1909: 1901: 1894: 1893: 1892: 1891: 1890: 1883: 1879: 1875:description, 1873: 1864: 1861: 1860: 1859: 1858: 1854: 1850: 1843: 1840: 1835: 1829: 1826: 1825: 1820: 1814: 1808: 1802: 1799: 1798: 1788: 1779: 1773: 1770: 1768: 1764: 1763: 1762: 1759: 1758: 1757: 1749: 1741: 1740: 1739: 1738: 1735: 1733: 1729: 1726: 1725: 1717: 1709: 1706:parameter to 1697: 1693: 1686: 1685: 1679: 1675: 1670: 1666: 1660: 1656: 1652: 1648: 1647: 1646: 1645: 1641: 1637: 1633: 1630: 1629: 1625: 1617: 1614:parameter to 1605: 1601: 1594: 1593: 1587: 1579: 1575: 1571: 1566: 1562: 1561: 1560: 1557: 1553: 1549: 1548: 1547: 1543: 1539: 1534: 1530: 1525: 1524: 1523: 1522: 1519: 1515: 1507: 1505: 1504: 1500: 1496: 1491: 1471: 1467: 1463: 1459: 1458: 1457: 1456: 1455: 1451: 1447: 1442: 1441: 1440: 1436: 1432: 1428: 1423: 1419: 1415: 1409: 1405: 1401: 1397: 1393: 1389: 1388: 1387: 1386: 1385: 1384: 1383: 1379: 1375: 1371: 1367: 1363: 1362:an additional 1359: 1355: 1354: 1353: 1352: 1351: 1350: 1345: 1341: 1337: 1332: 1331: 1330: 1329: 1326: 1322: 1318: 1314: 1311: 1307: 1303: 1302: 1301: 1300: 1296: 1292: 1278: 1275: 1274: 1273: 1272: 1270: 1267: 1266: 1264: 1261: 1252: 1249: 1248: 1247: 1246: 1244: 1241: 1240: 1238: 1235: 1226: 1223: 1222: 1221: 1220: 1218: 1214: 1211: 1210: 1208: 1205: 1204: 1200: 1196: 1192: 1188: 1183: 1176: 1173: 1170: 1167: 1163: 1160: 1157: 1153: 1149: 1148: 1146: 1143: 1142: 1140: 1137: 1132: 1129: 1128: 1126: 1123: 1118: 1114: 1111: 1110: 1108: 1105: 1104: 1103: 1097: 1091: 1087: 1083: 1079: 1074: 1071: 1067: 1062: 1059: 1056: 1053: 1050: 1047: 1044: 1041: 1038: 1035: 1032: 1029: 1026: 1023: 1022: 1020: 1019: 1018: 1017: 1014: 1010: 1006: 1002: 1000: 996: 992: 987: 983: 979: 975: 971: 970: 955: 951: 947: 942: 941: 940: 936: 932: 928: 927: 926: 925: 924: 923: 922: 921: 920: 919: 918: 917: 900: 896: 892: 887: 883: 882: 878: 875: 872: 869: 866: 863: 860: 859: 857: 856: 855: 854: 853: 852: 851: 850: 849: 848: 847: 846: 845: 844: 833: 829: 825: 820: 815: 814: 813: 812: 811: 810: 809: 808: 807: 806: 797: 793: 789: 784: 783: 782: 778: 774: 767: 760: 759: 758: 754: 750: 745: 744: 743: 742: 739: 735: 731: 724: 714: 707: 706: 705: 704: 700: 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1871:File:123.jpg 1846: 1833:File:123.jpg 1827: 1818:File:123.jpg 1812: 1806: 1800: 1794: 1752: 1751: 1747: 1730: 1727: 1721: 1715: 1707: 1696:edit request 1654: 1634: 1631: 1626: 1623: 1615: 1604:edit request 1556:Theanphibian 1518:Theanphibian 1511: 1489: 1487: 1421: 1417: 1395: 1391: 1369: 1365: 1361: 1357: 1309: 1305: 1288: 1276: 1268: 1262: 1250: 1242: 1236: 1224: 1212: 1206: 1165: 1155: 1151: 1144: 1138: 1130: 1124: 1112: 1106: 1101: 1072: 1065: 1060: 1054: 1051: 1048: 1042: 1036: 1030: 1024: 985: 981: 977: 973: 879: 873: 867: 861: 682: 665: 661: 584: 551: 528: 503: 481: 478: 455: 356: 297: 296: 272: 201: 172: 150: 129:User:WillowW 124: 111:User:WillowW 98: 85: 39: 31: 28: 20: 2303:User:Boghog 2165:" error fix 1661:. — Martin 1207:Argument 1. 1107:Argument 1. 666:destination 76:Proteopedia 66:NCBI Entrez 2275:|answered= 2141:|answered= 1700:|answered= 1608:|answered= 1263:Argument 3 1237:Argument 2 1139:Argument 3 1125:Argument 2 487:PDB enzyme 461:PDB enzyme 456:Note that 382:PDB enzyme 1636:MindZiper 1289:Cheers. 822:superior. 773:AndrewGNF 695:AndrewGNF 633:AndrewGNF 482:Clearly, 397:, and 5) 107:C2 domain 2301:Pinging 2237:Thanks! 1728:Thanks, 625:PDB link 615:PDB link 567:PDB link 534:PDB link 521:PDB link 372:PDB link 173:official 1495:Biophys 1462:Boghog2 1446:Biophys 1431:Biophys 1400:Boghog2 1374:Biophys 1336:Boghog2 1317:Biophys 1291:Boghog2 1187:Biophys 1082:Boghog2 1080:Cheers 1005:Biophys 991:Biophys 946:Boghog2 931:Biophys 891:Boghog2 824:Biophys 788:Boghog2 749:Biophys 648:Biophys 337:Biophys 303:Biophys 301:PDBsum. 240:Biophys 206:Biophys 157:Biophys 61:JenaLib 51:PDBWiki 42:PDBWiki 2361:Boghog 2355:: The 2307:Ahecht 2239:Boghog 2202:Boghog 2186:Boghog 2105:Boghog 2073:Boghog 2057:Boghog 1932:U+200B 1784:": --> 1570:Boghog 1538:Boghog 1066:BEFORE 662:format 180:??? -- 81:TOPSAN 56:PDBsum 2279:|ans= 2269:This 2145:|ans= 2135:This 1810:] ]] 1704:|ans= 1694:This 1655:Added 1612:|ans= 1602:This 1269:Reply 1243:Reply 1213:Reply 1145:Reply 1131:Reply 1113:Reply 718:into 539:into 506:like 504:looks 387:, 4) 377:, 3) 367:, 2) 151:Even 113:(see 2365:talk 2349:Done 2333:talk 2329:MSGJ 2315:PAGE 2313:TALK 2243:talk 2227:Done 2212:talk 2190:talk 2109:talk 2084:PDB2 2061:talk 2048:3TRA 2044:1OBB 2040:3BSE 2011:3TRA 2007:1OBB 2003:3BSE 1992:3TRA 1986:1OBB 1980:3BSE 1912:1LVM 1853:talk 1786:edit 1748:Done 1669:talk 1665:MSGJ 1640:talk 1574:talk 1565:edit 1542:talk 1533:2G9H 1499:talk 1466:talk 1450:talk 1435:talk 1422:that 1404:talk 1396:i.e. 1392:e.g. 1378:talk 1340:talk 1321:talk 1295:talk 1191:talk 1185:not. 1086:talk 1009:talk 995:talk 950:talk 935:talk 895:talk 828:talk 792:talk 777:talk 766:PDB2 753:talk 699:talk 652:talk 637:talk 601:PDB2 577:PDB2 544:PDB2 511:PDB3 450:1xyz 442:1xyz 434:1xyz 424:1xyz 417:1xyz 402:PDB3 392:PDB2 341:talk 323:talk 307:talk 298:None 244:talk 229:talk 210:talk 196:and 161:talk 125:much 99:four 17:link 2277:or 2143:or 2090:)? 2053:Lua 2036:PDB 1995:​) 1989:​, 1983:​, 1976:PDB 1908:PDB 1900:PDB 1882:123 1878:PDB 1849:a5b 1842:123 1839:PDB 1824:PDB 1722:to 1702:or 1657:to 1610:or 1536:​. 1529:PDB 1514:PDB 1490:and 734:Dan 713:PDB 670:Dan 587:Dan 572:or 557:PDB 526:. 497:PDB 471:PDB 430:PDB 413:PDB 362:PDB 182:Dan 153:MSD 140:Dan 88:Dan 71:OCA 46:); 2367:) 2331:· 2319:) 2283:no 2245:) 2214:) 2192:) 2149:no 2111:) 2087:}} 2081:{{ 2063:) 2046:, 2042:, 2038:: 2013:) 2009:, 2005:, 1978:: 1910:: 1903:}} 1897:{{ 1880:: 1855:) 1804:] 1708:no 1667:· 1642:) 1616:no 1576:) 1544:) 1531:: 1501:) 1468:) 1452:) 1437:) 1406:) 1380:) 1342:) 1323:) 1297:) 1219:. 1193:) 1152:22 1088:) 1011:) 997:) 986:2. 974:1. 952:) 937:) 897:) 830:) 794:) 779:) 769:}} 763:{{ 755:) 736:| 726:}} 720:{{ 716:}} 710:{{ 701:) 691:}} 685:{{ 672:| 654:) 639:) 628:}} 622:{{ 618:}} 612:{{ 604:}} 598:{{ 589:| 580:}} 574:{{ 570:}} 564:{{ 560:}} 554:{{ 547:}} 541:{{ 537:}} 531:{{ 524:}} 518:{{ 514:}} 508:{{ 500:}} 494:{{ 490:}} 484:{{ 476:. 474:}} 468:{{ 464:}} 458:{{ 432:: 415:: 407:; 405:}} 399:{{ 395:}} 389:{{ 385:}} 379:{{ 375:}} 369:{{ 365:}} 359:{{ 343:) 325:) 317:-- 309:) 246:) 231:) 223:-- 212:) 184:| 163:) 142:| 117:). 90:| 2363:( 2335:) 2327:( 2309:( 2241:( 2235:: 2231:@ 2210:( 2204:: 2200:@ 2188:( 2168:" 2161:" 2107:( 2075:: 2071:@ 2059:( 2029:: 2025:@ 1942:) 1938:( 1885:​ 1851:( 1790:] 1671:) 1663:( 1638:( 1572:( 1540:( 1497:( 1464:( 1448:( 1433:( 1402:( 1376:( 1338:( 1319:( 1293:( 1189:( 1156:3 1119:. 1084:( 1007:( 993:( 948:( 933:( 893:( 826:( 790:( 775:( 751:( 697:( 650:( 635:( 445:​ 437:​ 420:​ 339:( 321:( 305:( 242:( 227:( 208:( 159:(

Index

http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1xyz
http://www.rcsb.org/pdb/explore/explore.do?structureId=1XYZ
PDBWiki

PDBWiki
PDBsum
JenaLib
NCBI Entrez
OCA
Proteopedia
TOPSAN
Dan
09:59, 3 April 2008 (UTC)
Histone H2B type 1-C
C2 domain
User:WillowW
Category:Enzymes of known structure
User:WillowW
Dan
20:36, 3 April 2008 (UTC)
MSD
Biophys
talk
15:53, 3 April 2008 (UTC)
Comparison of online PDB derived databases
Dan
20:36, 3 April 2008 (UTC)
Protein structure databases
Protein sequence databases
Biophys

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