Tag Archives: news

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

Guest Post: New at VISTA- Inna Dubchak

Our first guest post in our new semi-regular Guest Post series is from Inna Dubchak , principal investigator at the LBNL/JGI group, developers of the VISTA comparative genomics resource (who sponsors a tutorial, free to the users). If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, please feel free to contact us at wlathe AT openhelix DOT com.

I would like to give you a heads up on some new VISTA updates and ongoing development!

Updates: As you probably know from this blog, a new, still free VISTA tutorial is available now. We have introduced a lot of updates to these tools - built new programs, improved the existing ones, and entirely changed the design of the site to make it more up-to-date and convenient.

Main addition to the site – VISTA Point – combines capabilities of the three tools currently available at the site – VISTA Gateway, VISTA Browser, and Text Browser usually used step-by-step. VISTA Point makes analyzing multiple and pairwise genome alignments and extracting relevant numerical data much more straightforward, it is easy to update, expand and add new programs.

Soon: We are actively working on visualizing synteny at scales ranging from whole-genome alignment to the conservation of individual genes, with seamless navigation across different levels of resolution. In our upcoming VISTA-Dot tool we used the concept of two-dimensional “dot-plots”, historically employed in the analysis of local alignment, and an interactive Google-map-like interface to visualize whole-genome alignments. You will be able to get a display and analyze large-scale duplication in plants in one click! It can also be useful in genome assembly and finishing. Another addition coming in the near future, VISTA Synteny Viewer, presents a novel interface as three cross-navigable panels representing different scales of the alignment.

Attention: do not forget to use our whole-genome capabilities – Whole-genome VISTA to align sequence of any quality, from draft to finished, up to 10MB long, and Whole Genome rVISTA to evaluate which transcription factor binding sites (TFBS) are over-represented in upstream regions in a group of genes.

-Inna Dubchak

RSS feeds

It can be really hard to keep up with the changes in the databases. We have joined all the support mailing lists (which we can discuss some other time), and they vary a lot in frequency and level of detail on changes at the different sites.

We are going to try to collect RSS feeds from useful sites that we want to monitor. We haven’t decided on a final look for them yet, but if you find an RSS feed for a site that would be useful, please let us know in the comments and we’ll add it to our collection.

PS: if you are a database or software provider and you don’t have an RSS feed for your news yet, please consider it. We’d like to have it.