Tag Archives: Entrez protein

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

New and Updated Online Tutorials for ASTD, Entrez Protein and MMDB

Comprehensive tutorials on the ASTD, Entrez Protein, and MMDB databases enable researchers to quickly and effectively use these invaluable variation resources.

Seattle, WA September 24, 2008 — OpenHelix today announced the availability of new tutorial suites on the Alternative Splicing and Transcript Diversity (ASTD) database, Entrez Protein and the Molecular Modeling Database (MMDB). ASTD is an European Bioinformatics Institute (EBI) resource for alternative splice events and transcripts for the human, mouse, and rat systems. Entrez protein is a comprehensive database of protein information brought to you by the National Center for Biotechnology Information (NCBI). MMDB is another NCBI resource which contains an extensive collection of three-dimensional protein structures with detailed annotation that can be used to learn about the structure and function of many proteins. Together these three tutorials give the researcher an excellent set of resources to carry their research from transcript to 3d protein structure.

The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

ASTD

  • to perform Quick and Advanced searches
  • to navigate gene and transcript report pages
  • to predict intron/exon boundaries and likely regulatory protein binding site
  • to search manually curated data regarding alternate splicing

Entrez Protein

  • to perform basic and advanced searches utilizing the many available tools and options
  • to understand the protein records and exploit the many internal and external links you are provided with
  • to explore some of the resources provided by the NCBI network of databases, such as “My NCBI”

MMDB

  • to search MMDB using both basic and advanced query techniques
  • to understand the detailed results you obtain
  • to visualize and manipulate structures using NCBI’s Cn3D structural viewer
  • to locate and view structurally aligned homologs

To find out more about these and other tutorial suites visit the OpenHelix Tutorial Catalog and OpenHelix or visit the OpenHelix Blog for up-to-date information on genomics.

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.