Tag Archives: SBKB

Video Tip of the Week: The PSI SBKB’s New Content Hubs


In today’s tip I will feature the newly organized content hubs over at the Protein Structure Initiative’s Structural Biology Knowledgebase, or PSI SBKB. We do have a free, full-length tutorial on the PSI SBKB that we are in the process of updating, but I thought I’d just touch on one of the new updates to the PSI SBKB now while it is “hot”. :) Quoting from their PSI: Biology in the Spotlight, July 2012 News:

This month, we release a new left menu which highlights our new scientific Hubs. These Hubs are designed to collect PSI and SBKB information so that our audience can find features based on their needs.

I’ve been working with these hubs over the last several months, and have gotten to watch as they have been developed. These scientific hubs make it easy for users to access specific content offered by both the SBKB and the PSI as a whole, because they are organized by content. I think the new left-hand organization is nice – the bright banner and organization will highlight these hubs to users, who will hopefully take full advantage of the resources found in each hub. Currently the scientific hubs are organized around the following content: targets; protein structures, sequences and function; membrane proteins; homology models; and methods. In the tip video I briefly visit the membrane proteins hub and the methods hub to give you an idea of the types of links and contents that you will find, but so be sure to check them out on your own to see what resources you can find for furthering your research.

For further details on the PSI SBKB, see the links below & stay tuned for our full, updated tutorial coming free to a browser near you! :)

Note: the open access papers will not cover the new hubs, but will describe many of the resources accessible from the hubs.

Quick links:
PSI Structural Biology Knowledgebase resource: http://www.sbkb.org

OpenHelix Introductory tutorial on the PSI SBKB (free to access):
http://www.openhelix.com/sbkb

Related resource – RCSB Protein Data Bank (RCSB PDB): http://www.rcsb.org

Related OpenHelix Introductory tutorial on the RCSB PDB (free to access):
http://www.openhelix.com/pdb

PSI SBKB References:

Gifford LK, Carter LG, Gabanyi MJ, Berman HM, & Adams PD (2012). The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. Journal of structural and functional genomics, 13 (2), 57-62 PMID: 22527514  (requires subscription)

Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, & Berman HM (2011). The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. Journal of structural and functional genomics, 12 (2), 45-54 PMID: 21472436 (open access here)

Cormier CY, Park JG, Fiacco M, Steel J, Hunter P, Kramer J, Singla R, & LaBaer J (2011). PSI:Biology-materials repository: a biologist’s resource for protein expression plasmids. Journal of structural and functional genomics, 12 (2), 55-62 PMID: 21360289 (open access here)

 

News Updates Related to the PDB (Protein Data Bank), etc.

This is a quick post to update you on events & news items that I’ve gathered that are associated with the Protein Data Bank and other protein resources.

  • We recently received a suggestion for the RCSB PDB through twitter:

    RT @27andaphd: @Comprendia @openhelix you know what? I really think the pdb should have a Firefox toolbar for struct bio ppl like me. cc @openhelix

Well , you are in luck, @27andaphd! I talked to someone on the PDB team and they have you covered with the toolbar, as described in this Summer 2010 newsletter item:  Search the RCSB PDB in Your Web Browser

  • The Structural Biology KnowledgeBase, or SBKB, is a sister database to the RCSB PDB, and last Thursday they released version 4.0 of the SBKB. I’ve been checking out the release & it looks good – they’ve organized categories of information and resources into “hubs”, such as a Structural Targets Hub, a Sequence, Structure, & Function Hub, a Methods Hub, and more. I’m in the process now of updating our sponsored (free) SBKB tutorial now, but you may want to check out the release & see what’s new.

  •  We’ll have more exciting news items soon, so stay tuned!

Quick links:
The Structural Biology KnowledgeBase (SBKB): http://www.sbkb.org/

The Protein Data Bank (PDB) http://www.pdb.org/

OpenHelix’s free introductory tutorial on the SBKB: http://www.openhelix.com/sbkb

OpenHelix’s free introductory tutorial on the PDB: http://www.openhelix.com/pdb

On a Mission for Protein Information

It’s probably just the human brain’s ability to connect dots  &  find patterns, but it can be interesting how many “unrelated” events and information bits accumulate in my head & eventually get mulled into an idea or theory. Take, for example, a recent biotech mixer, bits from an education leadership series & a past Nature article – each “event” has been meandering in my mind and now they are finding their way out as this blog post.

OK, now the explanation: At a recent local biotech event I heard about a company (KeraNetics) purifying keratin proteins & using them to develop therapeutic and research applications. The company & their research sounded very interesting & because a lot of it is aimed at aiding wounded soldiers, it also sounded directly beneficial. The talk was short, only about 20 minutes, so there wasn’t a lot of time for details or questions. I decided I’d venture forth through many of the bioscience databases and resources that I know and love, in order to learn more about keratin.

My quest was both fun and frustrating because of the nature of the beast – keratin is “well known” (i.e. it comes up in high school academic challenge competitions ‘a lot’, according to someone in the know), but is hard to work with (i.e. tough, insoluble, fibrous structural proteins) that is hard to find much general information on in your average protein database (because it is  made of many different gene products, all referred to as “keratin”). I decided to begin my adventure at two of my favorite protein resources, PDB & SBKB, but I found no solved structures for keratin. Because of the way model organism databases are curated and organized, I often begin a protein search there, just to get some basic background, gene names, sequence information, etc. I (of course) found nothing other than a couple of GO terms in the Saccharomyces Genome Database (SGD), but I found hundreds of results in both Mouse Genome Informatics (MGI) (660 genomic features) and Rat Genome Database (RGD) (162 rat genes, 342 human genes). I also found gene names (Krt*), sequences and many summary annotations with references to diseases with links to OMIM. When I queried for “keratin”, in OMIM I got 180 hits, including 61 “clinical synopsises”, in UniProt returned 505 reviewed entries and 2,435 unreviewed entiries, in Entrez Protein 10,611 results and in PubMed 26,430 articles with 1,707 reviews. I got my curiosity about KeraNetics’ research sated by using a PubMed advanced search for Keratin in the abstract or title & the PI’s name as author (search = “(keratin[Title/Abstract]) AND Van Dyke[Author]“).

I ended up with a lot of information leads that I could have hunted through, but it was a fun process in which I learned a lot about keratin. This is where the education stuff comes in. I’ve been seeing a lot of studies go by talking about reforming education to be more investigation driven, and I can totally see how that can work. “Learning” through memorization & regurgitation is dry for everyone & rough for the “memory challenged”, like me. Having a reason or curiosity to explore, with a new nugget of data or understanding lurking around each corner, the information just seems to get in better & stay longer. (OT, but thought I’d mention a related site that I found today w/ some neat stuff: Mind/Shift-How we will learn.)

And I could have done the advanced PubMed search in the beginning, but what fun would that have been? Plus there is a lot that I learned about keratin from what I didn’t find, like that there wasn’t a plethora of PDB structures for keratin proteins. That brings me to the final dot in my mullings – an article that I came across today as I worked on my reading backlog: “Too many roads not taken“. If you have a subscription to Nature you can read it, but the main point is that researchers are still largely focusing on the same set of proteins that they have been for a long time, because these are the proteins for which there are research tools (antibodies, chemical inhibitors, etc). This same sort of philosophy is fueling the Protein Structure Initiative (PSI) efforts, as described here. Anyway, I found the article interesting & agree with the authors general suggestions. I would however extend it beyond these physical research tools & say that going forward researchers need more data analysis tools, and training on how to use them – but I would, wouldn’t I? :)

References:

  • Sierpinski P, Garrett J, Ma J, Apel P, Klorig D, Smith T, Koman LA, Atala A, & Van Dyke M (2008). The use of keratin biomaterials derived from human hair for the promotion of rapid regeneration of peripheral nerves. Biomaterials, 29 (1), 118-28 PMID: 17919720
  • Edwards, A., Isserlin, R., Bader, G., Frye, S., Willson, T., & Yu, F. (2011). Too many roads not taken Nature, 470 (7333), 163-165 DOI: 10.1038/470163a

Tip of the Week: From UniProt to the PSI SBKB and Back Again


It is often beneficial to visit multiple biomedical databases or resources, even if they seem to provide overlapping  information because no two resources focus on the exact same information, or present it in exactly the same way. Instead of duplicating each others’ curation efforts, database often link out to related information at other resources. You can think of these links as “social connections”, if you want and in today’s tip I want to show you a couple of connections between protein information resources, including a new connection that really features some of the core value of the PSI’s Structural Biology Knowledgebase, or SBKB.

I begin the tip at the UniProtKB, where I search for a UniProt ID number. From the resulting protein report I first briefly show you how to link out to a corresponding RCSB PDB report, where you can find high quality protein structure information and more. If you are interested in learning more about the RCSB PDB & how to use it, please check out OpenHelix’s full, free tutorial that is sponsored by the RCSB PDB.

From there I return to the UniProt report and demonstrate a new link out option that links to protein protocols, available materials, as well as information about theoretical models and predicted protein targets from the SBKB. I don’t have time to show it but a recent update to the SBKB allows users to now search the Structure Biology Knowledgebase with a UniProt accession number. These searches provide users with additional information including protein structure information and information about pre-released structure sequence. As with the RCSB PDB, we have a free tutorial on the SBKB that is sponsored by the Protein Structure Initiative.

As I scroll through the UniProt protein report users will see information and links for a wide variety of bioscience resources. OpenHelix, as I’m sure many of you are aware, has tutorials on how to use many of these resources. Our tutorials on the RCSB PDB and the PSI SBKB are both free. Our tutorials on UniProt and many other resources are available through a subscription to our database of trainings or through purchase of individual access. Whether you learn the resources through our tutorials, through the references I list below, or through your own explorations of the databases, there really is an amazing amount of information available through these interlinked, publicly-funded resources – please make use of them in your research!

Quick Links:

UniProt Knowledgebase -  http://www.uniprot.org/

OpenHelix Tutorial on UniProt – http://www.openhelix.com/cgi/tutorialInfo.cgi?id=77

RCSB PDB – http://www.pdb.org

OpenHelix Tutorial on the RCSB PDB – http://www.openhelix.com/pdb

The Protein Structure Initiative Structural Biology Knowledgebase (SBKB) -  http://www.sbkb.org/

OpenHelix Tutorial on the SBKB – http://www.openhelix.com/sbkb

Catalog of all OpenHelix tutorials – http://www.openhelix.com/cgi/tutorials.cgi

References:
The UniProt Consortium. (2009). The Universal Protein Resource (UniProt) in 2010 Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp846

Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J., Young, J., Yukich, B., Zardecki, C., Berman, H., & Bourne, P. (2010). The RCSB Protein Data Bank: redesigned web site and web services Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq1021

Berman, H., Westbrook, J., Gabanyi, M., Tao, W., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L., Kopp, J., Podvinec, M., Adams, P., Carter, L., Minor, W., Nair, R., & Baer, J. (2009). The protein structure initiative structural genomics knowledgebase Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn790

The Protein Structure Initiative Announces an Updated Free OpenHelix Tutorial and Training Materials for the Structural Biology Knowledgebase (SBKB).

Free tutorial suite on the Structural Biology Knowledgebase includes an online narrated movie, PowerPoint slides, slide handouts and exercises.

Bellevue, WA (PRWEB) April 11, 2011

The Structural Biology Knowledgebase (SBKB), a one-stop shop for information about proteins hosted at Rutgers University, has partnered with OpenHelix to provide an updated and revised free tutorial suite (http://www.openhelix.com/sbkb) on its online protein “portal” located at http://sbkb.org/.

The SBKB is a free, comprehensive resource produced through a collaboration between the National Institutes of Health’s Protein Structure Initiative: Biology program and the Nature Publishing Group. The PSI SBKB contains genetic, structural, functional and experimental information about proteins that is easily accessible through a variety of reports and displays. The portal also includes links to many additional resources.

The new tutorial reflects the many changes and enhancements to the SBKB, including a recent name change from Structural Genomics Knowledgebase to Structural Biology Knowledgebase, new navigation organization, and remodeled Protein Model Portal reports, among many others.
The online narrated tutorial runs in just about any browser and can be navigated in a number of ways. In about 60 minutes, the tutorial highlights and explains the features and functionality needed to start using the SBKB effectively. The tutorial can be used by new users to introduce them to the protein portal, by previous users to view new features and functionality, or simply as a reference tool to understand specific features.

In addition to the tutorial, users can also access useful training and teaching materials including the animated PowerPoint slides used as a basis for the tutorial, suggested script for the slides, slide handouts, and exercises. This can save a tremendous amount time and effort for teachers and professors to create classroom content.

Users can view the tutorials and download the free materials at http://www.openhelix.com/sbkb.

About the PSI
The Protein Structure Initiative (PSI, http://www.nigms.nih.gov/Initiatives/PSI/psi_biology/), which is supported by the National Institutes of Health, is a federal, university and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure. The long-range goal of the PSI is to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. The PSI strives to gain biological insights from new structures and to help the broad biomedical research community make use of PSI research findings.

About OpenHelix
OpenHelix, LLC, (http://www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to over 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Protein Structure Analysis – How Far We’ve Come!

The team here at OpenHelix has recently updated our sponsored tutorials on two excellent structural biology resources, the RCSB Protein Data Bank (PBD) and the PSI-Nature Structural Biology Knowledgebase (PSI SBKB). Because the tutorials are sponsored by these resources they are free for anyone to view and download in full. You can access our training materials for the resources at our RCSB PDB landing page, or our PSI SBKB landing page. I’m very happy with both tutorial suites, so please check them out.

As my personal celebration for these releases I have been reading a variety of articles showing the scope of how far our abilities to analyze protein structures have come. The first article is one that Mary pointed me to a while back, which discusses the infancy of bioinformatics, entitled “The Roots of Bioinformatics in Protein Evolution” by RF Doolittle (cited below, as are all articles mentioned). In this wonderful perspective Dr. Doolittle describes a time when DNA sequencing was unimaginable and protein sequencing was laborious, slow, and yet so new that each day was full of excitement as one more amino acid was identified. It is a revealing glimpse at a research era gone by – to quote Doolittle, “Science as an endeavor thrives on obsolescence.” – and mentions the contributions of Margaret Dayhoff, who Mary has blogged about.

The next historical article that I read was entitled “The Early Years of Retroviral Protease Crystal Structures” by M Miller (freely available on PMC). As you can tell from the title, this covers a time more recent than the Doolittle article, when protein crystallization studies were possible. Dr. Miller traces the X-ray crystal studies of retroviral proteases at the NCI-Fredrick in the late 1980′s and early 1990′s, and she describes how chemical synthesis of HIV1-PR was critical to obtaining enough protein for crystallization and how the crystal structure of it (deposited into the PDB archive and therefore freely available for all researchers to study) was invaluable for the design of inhibitors of HIV1-PR as anti-AIDS drugs.

I’ve also be perusing more recent papers that highlight how protein structures can aid biological investigations. These include: “Structure of mammalian AMPK and its regulation by ADP“,  “Bioinformatics analysis of disordered proteins in prokaryotes“, “Crystal structure of inhibitor of κB kinase β” and others. It would also be fun to attend “The 25th Annual Meeting of the Groups Studying the Structures of AIDS-Related Systems and Their Application to Targeted Drug Design” to learn more, but alas I will not be in the area at the time of the meeting. As I’ve posted before, I am a geneticist by education. To me seeing the development of protein studies (through the historical reviews) and the studies currently occurring in the field of structural biology, combined with the amazing offerings available freely through both the RCSB PDB and the PSI SBKB really does feel like an appropriate, and enjoyable, celebration for the completion of our tutorial updates. Let me know what you think about them, when you get a chance! :)

Updated freely available sponsored tutorials; movie, slides, exercises to use:

References:

  • Berman, H. (2000). The Protein Data Bank Nucleic Acids Research, 28 (1), 235-242 DOI: 10.1093/nar/28.1.235
  • Berman, H., Westbrook, J., Gabanyi, M., Tao, W., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L., Kopp, J., Podvinec, M., Adams, P., Carter, L., Minor, W., Nair, R., & Baer, J. (2009). The protein structure initiative structural genomics knowledgebase Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn790
  • Doolittle, R. (2010). The Roots of Bioinformatics in Protein Evolution PLoS Computational Biology, 6 (7) DOI: 10.1371/journal.pcbi.1000875
  • Miller, M. (2010). The early years of retroviral protease crystal structures Biopolymers, 94 (4), 521-529 DOI: 10.1002/bip.21387

SBKB – New Name, Same Great Resource + More!

The PSI-Nature Structural Genomics Knowledgebase (SGKB) that we’ve posted on before has been rebranded to now be named the PSI-Nature Structural Biology Knowledgebase (SBKB), provided to you by the Protein Structure Initiative (PSI). The new branding just rolled out yesterday, along with the September issue of all the features, and a reorganized left navigation area that organizes pages by scientific focus.

But don’t fear, the FREE SGKB tutorial by OpenHelix that you know and love still accurately demonstrates how to use the search functions of the SBKB, and we are currently working to update our tutorial to reflect the new branding and the new navigation options. Stay tuned for an announcement about the release of the updated SBKB tutorial soon!