Tag Archives: PDB

RCSB PDB and OpenHelix Announce an Updated Free Tutorial and Training Materials

The new tutorial reflects the many changes and enhancements on the RCSB PDB site, and includes a narrated on-line tutorial, PowerPoint slides, handouts, and exercises.

Bellevue, WA (PRWEB) April 12, 2011

The Research Collaboratory for Structural Biology (RCSB) Protein Data Bank (PDB) has partnered with OpenHelix to provide a revised and updated tutorial (http://www.openhelix.com/PDB) on its free web based resource for studying biological macromolecules (http://www.pdb.org).

The RCSB PDB provides a variety of tools and resources to use to study biological macromolecules. The PDB is the single worldwide repository of experimentally-determined 3D biological structures of proteins, nucleic acids and complex assemblies. As a member of the Worldwide PDB collaboration (wwpdb.org), the RCSB PDB curates and annotates PDB data, and presents basic and advanced search, display and visualization methods to access these data.

The new tutorial reflects the many changes and enhancements on the RCSB PDB site, including a new data drill-down and data summary feature, updated ligand features such as a download page, images and binding affinity data, new report types and visualization options, among many others.

The new training materials (at http://www.openhelix.com/pdb) include an online narrated tutorial that demonstrates: basic and advanced searches, how to generate reports, the different options for exploring individual structures, and many of the research and educational resources and tools available at the RCSB PDB. The approximately 60-minute tutorial, which runs in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders.

In addition to the tutorial, RCSB PDB 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 tutorial and download the free materials at http://www.openhelix.com/pdb.

About the RCSB PDB
The RCSB Protein Data Bank (http://www.pdb.org), administered by the Research Collaboratory for Structural Bioinformatics (RCSB), supports scientific research and education worldwide by providing an essential resource of information about biomolecular structures. These molecules of life are found in all organisms, from bacteria and plants to animals and humans.

The RCSB PDB member institutions jointly manage the project: Rutgers, The State University of New Jersey and the San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego.

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 nearly 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

Tip of the Week: RCSB PDB Data Distribution Summaries


In today’s tip I will feature the data distribution summaries and their drill down features which you can see from many RCSB PDB searches. We are in the process of updating our full tutorial sponsored by the RCSB PDB team, and as part of that effort I’ve gotten to know and appreciate this new data presentation format. Over the last five years the RCSB PDB has really been working hard at redesigning their resource to be more easily accessed by a wide variety of users. Below you will find a recent citation from the group explaining all of their updates and the logic behind them. The paper is a good read because I won’t have time to do anything except scratch the surface of the redesign & you’ll get the details there, but also because  the intro also gives a great glimpse into what resources are dealing with in the way of ‘data deluge’. The increase in users AND data that the RCSB PDB has experienced over the last few years is mind boggling!

OK, back to the data distributions. To me these are really elegant ways of helping any user – PDB is by no means just for structural biologists – come to the RCSB PDB & quickly and easily access whole categories of interesting information and then drill down in detailed ways to access the specific structure or data that they are most interested in.  For example, I could begin with a keyword search for something as general as ‘kinase’. This search retrieves over 4 thousand hits, which could be quite daunting, but at the top of the report results are displayed under categories such as Organism, Taxonomy, Experimental Method, SCOP classification and more. Subcategories under each of these categories lets me know how many hits are, for example are a mixed Polymer type, are human hits, or are alpha and beta proteins. I can mouse over any subcategory title to find out the percent of hits in this category compared to all hits, or click on the title to further drill-down the data distribution on just that subcategory of results. The distribution summaries are updated to then focus specifically on the distribution of THOSE data. Using these summaries is much more intuitive than any text description description that I can muster.

My advice? Check out the tip, then check out the data distribution summaries, drill down utility, and all the other great features of the RCSB PDB & see how easy it is to find information on your favorite gene. Oh yea, and be watching for us to release our full, free & newly updated tutorial on the RCSB PDB resource soon!

ResearchBlogging.orgRose, 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

Education at NCBI

I’d like to point out the new NCBI Education page. There is a lot there that you might want to check out. NCBI will be, starting this fall, offering a series of two-day training courses they are calling Discovery Workshops. Two years ago they ended the NCBI Field Guide workshops, so this seems to be a welcome change.

There are also webinars. Our research suggests that webinars are not particularly popular, so I’m curious how these turn out. There are also ‘how-to’ guides, documentation, community, teacher resources. It’s quite a nice site with lots of things to check out.

I’d also like to point out the “recommended links” section. There are lots of links to additional educational resources like the Cold Spring Harbor’s Dolan DNA Learning Center and much more. And, incidentally :), a link to our own free tutorials which was very nice to see. You might want to check those out, we have over 10 including PDB, SGKB, UCSC Genome Browser, Galaxy, several model organism databases, and more.

Tip of the Week: WAVe, Web Analysis of the Variome

Today’s Tip of the Week is a short introduction to WAVe, or the Web Analysis of the Variome. The tool was recently introduced to us, and I’ve found it a welcome introduction to the tools available to the researcher to analyze human variation. This is apropos considering the recent paper we’ve been discussing on the clinical assessment of a personal genome (here, here and here) and that papers implications for personalized medicine and the use of online variation resources. WAVe also has introduced me to some additional tools I’ve either not been aware of, or haven’t used, which might be of use such as: LOVD (Leiden Open Variation Database), QuExT (Query Expansion Tool, also from the same developers as WAVe), and others. Of course there are also database information pulled in from Ensembl, Reactome, KEGG, InterPro, PDB, UniProt, NCBI and many others. Take some time to check it out.

RCSB PDB Teams with OpenHelix to Announce Free Tutorial and Training Materials

The Protein Data Bank (PDB) bioinformatics resource partners with OpenHelix to provide online tutorial suite, Quick Reference Cards, and other training and outreach programs.

Seattle, WA (PRWEB) April 13, 2010 — The Research Collaboratory for Structural Biology (RCSB) Protein Data Bank (PDB), has partnered with OpenHelixTM to provide comprehensive training and outreach programs for its free, web-based resource (www.pdb.org).

The RCSB PDB provides a variety of tools and resources to use to study biological macromolecules. The PDB is the single worldwide repository of experimentally-determined 3D biological structures of proteins, nucleic acids and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data, and presents basic and advanced search, display and visualization methods to access these data.

“RCSB PDB is a premier resource with a long history of providing researchers with excellent data and tools,” said OpenHelix founder and President Dr. Mary Mangan. “We are proud to be able to contribute to the effort to increase users’ access and understanding of these tools.”

The new training tools (at http://www.openhelix.com/pdb) include an online narrated tutorial that demonstrates: basic and advanced searches, how to generate reports, the different options for exploring individual structures, and many of the research and educational resources and tools available at the RCSB PDB. The approximately 60-minute tutorial, which runs in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders.

In addition to the tutorial, RCSB PDB users can access useful training 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.

OpenHelix also has created free Quick Reference Cards for the RCSB PDB. The Quick Reference Card highlights features found on the home page, as well as search strategies, features, and functionalities. The cards can be ordered at www.openhelix.com. Thirty cards can be ordered at a time and shipping is free within the United States.

“We are pleased to team with OpenHelix to offer these new training materials alongside their other great bioinformatics resource tutorials,” said Helen M. Berman, Director of the RCSB PDB. “The suite of materials can introduce new users to the RCSB PDB and serve as a quick reference for our experts.”

Users can view the tutorials and download the free materials at www.openhelix.com.

About the RCSB PDB
The RCSB Protein Data Bank (www.pdb.org), administered by the Research Collaboratory for Structural Bioinformatics (RCSB), supports scientific research and education worldwide by providing an essential resource of information about biomolecular structures. These molecules of life are found in all organisms, from bacteria and plants to animals and humans.

The RCSB PDB member institutions jointly manage the project: Rutgers, The State University of New Jersey and the San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego.

About OpenHelix
OpenHelix, LLC, (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 nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Quick note: SGKB and PDB tutorials

We recently announced a free tutorial (sponsored by PSI) on the Structural Genomics Knowledgebase (SGKB). I thought it might be of interest to our readers. You can access the free tutorial (approx. a 1hr movie, slides, handouts and exercises) here.

We will also soon announce a free tutorial on the Protein Database (PDB), but you can already access it here.

For a full list of our free tutorials and training materials, click here (about a dozen), or view our other 80 or more tutorials on a wide range of topics by subscription.

Tip of the Week: Year of Tips, part deux

As Trey posted last week in part I, we’ve been doing tips-of-the-week for two years now. We have completed over 100 little tidbit introductions to various resources*.  At the end of the year we are doing a summary post to collect them all.  If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

I’ve got the second half of this year to summarize–July through December 2009. Check them out!

July 2009

7/1  UCSC wiki annotations UCSC has created a way for anyone to add annotations to their genes of interest using a wiki.

7/8  CellMiner from NCI A relational database for cancer cell line data.

7/15  ENCODE data at UCSC The Data Coordination Center, or DCC, for the human ENCODE data is introduced, with guidance on how to access ENCODE data in the UCSC Genome Browser.

7/22  It’s a duplicate Check out Deja Vu, a program to assess scientific abstracts for similarity, including duplication or possible plagiarism events.

7/29 VirusMINT The Molecular Interaction Database that we love added a component for Virus protein interactions.

August 2009

8/5  Genomic Encyclopedia of Bacteria & Archaea (GEBA) This piece on the strategy of choosing new genomes to sequence was introduced in August.  If this is of interest to you, also check out the recent publication about this project that we talked about here.

8/12  NCBI’s New BioSystems Resource Wherein NCBI takes on the storage and representation of biological network data.

8/19  PLAN2L for Arabidopsis literature A helpful tool for literature searching for Arabidopsis.

8/26  Acytelome, String and a new database An introduction to the Phosida database, for phosphorylation and acetylation information.

September 2009

9/2 A mouse for all reasons Learn about the knockoutmouse.org site, which provides information and reagents for generating knockout mice.

9/9  TARGeT A resource for identifying transposable elements and genes relationships from sequence submissions.

9/16  The National Center for Biomedical Ontology This central repository for Ontologies can be really helpful for bioinformatics software project developers.

9/23  JBrowse, a game changer? A look at a new strategy in genome browsing software.

9/30  Finding the right genomics resource This is a quick introduction to OpenHelix’s own new interface for searching for training movies and materials!

October 2009

10/7  NCBI Makeover! The overhaul of the NCBI interface–with a walk through memory lane at some of it’s previous incarnations–is provided.

10/14  Getting flanking sequence A quick look at how to use Galaxy to obtain adjacent sequences, which is a question we are asked frequently in training situations.

10/21  SwissVar, a New Genotype-phenotype Resource from SIB Explore ‘a portal to Swiss-Prot diseases and variants.’

10/28  Sol Genomics Network Do you like tomatoes, eggplants, potatoes, peppers, and other members of the Solanaceae? If so, check out this resource.

November 2009

11/4  CHOP CNV database If you are curious about copy-number variations, be sure to explore the collection at CHOP.

11/11  GeVo and Genome Comparison A nifty tool for genomic comparisons.

11/18  FABLE, text mining for literature on human genes A literature mining resource to improve you searching.

11/25  Got tips for us? We opened the floor for suggestions of tools to look at as we celebrated the Thanksgiving holiday.  We’ll still take suggestions–we love to explore new resources!

December 2009

12/2  RCSB PDB Comparison Tool Compare sequences for structural similarities with this handy widget.

12/9  GRAIL for prioritizing SNPs Use a list of SNPs to identify associated genes, and then sweep the literature for leads on the processes that might be involved.

12/16  GenomePad Check out this very cool iPhone app for exploring the UCSC Genome Browser.

12/23  Tip of the Week: Year (2nd!) of Tips for the first half of the year’s summary of tips.

*for the vast majority of resources we introduce in our tips, we have no financial relationship with the provider or developer. The ones we do are listed here.

Tip of the Week: RCSB PDB Comparison Tool

2009-12-01_PDB_comptoolIn today’s tip I am going to feature a sequence and structure comparison tool brought to you by the RCSB Protein Data Bank, or PDB. The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data, and provides a variety of tools and resources to accessing these data.

I’m sure MANY of you are familiar with the RCSB PDB and rely on them to provide you access to protein structures. If you haven’t visited the RCSB PDB lately, you may be surprised to see how many features and functions they’ve updated and added. We are currently updating our tutorial on this great resource. When it is ready the tutorial will show you where to find many of these updates and how to use them. I’m sure we’ll announce the release of our updated materials, but for now I’m going to provide you with a RCSB PDB ‘teaser’ that I hope will entice you to into visiting and exploring the RCSB PDB, as well as watching for our updated tutorial.

And if after seeing this tip you think you might want to have an easy way to access this tool, you can add it to your own blog or lab homepage just by getting the widget code, as described in this post by Trey.  Enjoy this weeks tip!

Widgets are cool

RCSB has put goether a PDB Comparison Tool Widget .


I put in 2K9G and 1ZLM, two SH3 domains. Used chain A for both and blast2seq as comparison algorithm (there are several choices), and these are my results. I’m not promising any biological significance to my choices and results, but the widget works nicely and simply. I can see it as a nice addition to someone’s homepage.

There are some other 3rd party widgets over at PDB such as this SGKB widget which you can get at the link above and the Mac dashboard widget you can download (and I always like Mac biology widget!).

Which got me to thinking, there must be other widgets out there for embedding into web sites. I found this Ontology one, anyone else know of any? Perhaps I can put together a widget page! for fun.