Tag Archives: ExPASy

Many Protein Resources Have Recently Announced Updates

PDB structure 3rg9





In our ongoing pursuit of up-to-date tutorials, I’ve been tracking changes that are occurring at resources and planning our updates accordingly. Protein resources are especially going to keep me out of trouble this summer, because their developers and curators have been busy! I’ve compiled a short synopsis below, and would appreciate comments on any other resources you know about, or want to brag about! :)

  • I featured the ExPASy list of proteomic tools in a past tip. As of  Tuesday this list is no longer being kept up-to-date, but the ExPASy resource has been expanded beyond being “just” a proteomics resource and is now the new SIB Bioinformatics Resource Portal. According to its developers, the portal:

    “provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. … On this portal you find resources from many different SIB groups as well as external institutions.”

    And never fear, there is still an up-to-date list of proteomics tools found here.

  • I mentioned in my tip last week that NCBI’s MMDB has undergone an update & I’ll be updating our tutorial on it soon.
  • NCI/Nature Pathway Interaction Database, or PID, had an update June 14th that includes new and updated pathway information.
  • PROSITE had an update June 21st, which is Release 20.73, and now includes 1618 documentation entries, 1308 patterns, 936 profiles and 925 ProRules.
  • The RCSB PDB resource has announced updates to their Browse Database function, enhanced sequence displays from structure summary pages and the PDB-101 educational resource available from blackboard logos on PDB pages. For more details on using PDB, please see our free PDB Introductory tutorial sponsored by the RCSB.
  • STRING’s 9.0 release is now available, and we’ll be looking into anything we need to update in our tutorial as a result.
  • UniProt released an update June 28th that included a major update on many bacterial and archaeal Type II Toxin-Antitoxin modules, as is described here.

Enjoy all the new information – I know I will! :)

GlycoSuiteDB back online

Out at a recent training I was talking to a scientist about resources for protein modifications–specifically glycans.  There are special challenges and complexities about studying these residues and I was trying to direct him to resources that might offer some information.  And then just last week I got notice that GlycoSuite is back online.  So I thought I would mention that today:

From the Swiss-Flash mailing list on 5/29/09:

GlycoSuiteDB is back online
By Christine Hoogland

The Swiss Institute of Bioinformatics is pleased to announce the re-launch of GlycoSuiteDB, a product of Tyrian Diagnostics Ltd (formerly Proteome Systems Ltd). Thanks to this collaboration the glycan database is available in open access on the ExPASy website.

GlycoSuiteDB is a curated and annotated glycan database. The current Release 8.0 contains 9436 entries, sourced from 864 references. The content of the database was transcribed as is but will expand again. Within the next months new data relative to bacterial sugars will be included. In the coming year the database will evolve through collaborative work with glycobiologists including Prof. N. Packer who initiated the GlycoSuiteDB project. The database is now available from a new URL, you are welcome to update your bookmarks and websites accordingly:

So go get sugared up!

Tip of the Week: ViralZone at ExPASy

viralzone_tip For today’s tip I am going to continue with the theme I started yesterday – obtaining swine flu information. There are many wonderful viral resources that are publicly available. I  linked to NCBI’s Influenza Virus Resource in yesterdays post, and you can watch past tips that Trey has done tips on the Viral Bioinformatics Resource Center (VBRC) here and here. But for todays tip I’ve like to introduce you to the ViralZone, which is available from the ExPASy Proteomics Server.  ViralZone is  created by the Swiss Institute of Bioinformatics (SIB) and provides a really clear, concise introduction to a virus as well as links to any variety of detailed information.

Tip of the Week: Collection of Proteomics Tools at ExPASy, including Radar

I’ve blogged about ExPASy in the past, and today my tip is based at this WONDERFUL site. In the tip I will briefly introduce you to a list of proteomic tools that cover a wide range of functions you may need to apply to your favorite sequence or sequences, and demonstrate one such tool. These tools are both from the ExPASy team and from other providers. Each tool is described and links to it are provided. The tools are organized into categories of functions for easier perusing of the list. I feature a repeat finder named Radar.

If you find one you love (or can’t live without) in this list PLEASE do let us know!  Happy proteomics to you!

Catching up on Newsletters: Biocurator & SwissProt Updates

Time to ReadOh I know that I should read all the newsletters that I get when they are fresh and new, but in the heat and hurry of life I don’t always do what I should. So last night while my husband was at golf league & my daughter was ‘Nintendo-ing’, I read. And some of what I read was so cool I just had to over come the embarrassment of admitting my reading back-log to spread the word.  The first bit isn’t actually that old – the email was from Monday.  It was from the Biocurator’s mailing list & announced the formation of the International  Society for Biocuration (ISB) and that the next International Biocurator Meeting will take place in spring 2009 in Germany under the helm of the International Biocuration Society. You can read the full announcement here.

GermanyI find this really exciting for many reasons. First, I attended both the First and Second International Biocurator Meetings and I can not tell you how good those meetings were – just massively cool exchange of ideas – so the idea of getting to go to Germany to attend the third one makes me about giddy. Second, I am really excited about the professional society. I was a biocurator for years and still consider myself as ‘part of the team’ (I work hard everyday trying to teach people about the incredible resources biocurators are making & do regularly send feedback & bug reports to databases). I am so proud of the career that I am encouraging one of my cousins to join our ranks. Having a professional society to call our own will raise the profession even higher, in my humble opinion. Third, the society will be based in Geneva Switzerland, where the UniProt/Swiss-Prot group will provide essential support. Why is that interesting? Well, aside from the fact that I think the group at Swiss-Prot will do a great job, it also is a great lead in for the second news item that I want to draw your attention to.

ExPASy CelebrationThis one is a bit older – actually from a Swiss-Flash bulletindated April 21, 2008. It announced the 15th anniversary celebration of ExPASy, and ExPASy is celebrating with a user survey. Now if you love ExPASy like I do (they are my first source for figuring out ENZYME nomenclature & I’ve blogged about their Protein Spotlight & commented on their Swiss Quiz in the past)  please be sure to celebrate with them by filling out their user survey, which is still open.