Tag Archives: RCSB PDB

RCSB PDB Webinar follow-up post: further questions?

The February 15th “How to use the RCSB Protein Data Bank” webinar may generate some questions that we won’t have time to cover or there may be further questions that arise. So we’ll leave this blog post open for follow-up on issues that arise from our discussion. Feel free to add your questions as comments to the post.

The slides from that webinar are available here:

RCSB PDB tutorial and training materials

If you didn’t have a chance to fill out the survey, here’s the link: http://www.surveymonkey.com/s/3WZSR98

Questions from the webinar chat:

1.  We were asked about differences in what I was showing in my screenshots, and what people were seeing on RCSB PDB pages. There are two possible reasons that this might be.

The first reason is that not all structures are associated with all types of information. For example, if you compare the 2ara structure summary page to the 2arc structure summary page you will notice that the 2ara page is the apo form of the molecule and does not have a ligand, a “Ligand Chemical Component” area, or an area for External Ligand Annotation information. The 2arc structure is bound to its ligand, alpha-L-arabinose (or ARA) and so it does have both Ligand Chemical Component area and an area for External Ligand Annotation on its page. The information that you see on various RCSB PDB pages will depend on what is available for the specific entry that you are looking at.

The second reason is a bit more trivial, but equally important – RCSB PDB pages are constantly being updated, and so while the screenshots in our training materials do accurately represent the overall organization and features of resource pages, specific numbers, reference lists, etc. may change over time from what our screenshots show. We work closely with the RCSB PDB developers to keep our materials up-to-date with major software updates that would dramatically change functionality of the tools we present.

2. Another great set of questions that we got during the webinar is whether people could use our materials for their students, and where to download our free training materials on the RCSB PDB.

We would be delighted if our materials were used to teach students, or were presented as a group meeting, etc – really any non-profit use of our freely available materials is fine by us – as long as you don’t remove our copyright notices. We often “train the trainer” in our live seminars or webinars, who then go out and further the reach of our materials by using them to train others at their institutions. And we’ve heard that our materials are great to use in a classroom because not only do we offer the online modular tutorial movie that can be watched online from any browser, we also provide PowerPoint slides with the full script text, handouts for note taking, and an exercise document that can be handed out as a class assignment, or used for a classroom “walk through” discussion.

All that leads to the next part of the question, where can I download OpenHelix’s free training materials on the RCSB PDB? You can download materials free of charge, and without registering at our RCSB PDB tutorial landing page. Just click any of the buttons on the page to 1) launch the movie, 2) download any of our materials, or 3) visit the RCSB PDB resource.


Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • Snorf. RT @szintri: “underappreciated fact of genome assembly…the choice of assemblers is often limited to those that run without crashing” via @JChrisPires [Mary]
  • RT @yokofakun: the correct URL for VARMD is http://t.co/AvNWueQU  “analyzing the DNA sequence variants produced by human exome sequencing” [Mary]
  • Found this GenomeWeb article interesting – Lot to think about/figure out: “White House Bioethics Commission Tackles Genomic Data” [Jennifer]
  • RT @drbachinsky: Personal genomes hold eventual promise for treatments – Mass High Tech Business News http://t.co/PQFqqbPf [Mary]
  • I’m working on my ScienceOnline2012 report(s), but in the meantime check out this list of blog and media coverage from before, during and after the conference here. [Jennifer]
  • Don’t forget to register & attend our free ‘How to use the RSCB Protein Data Bank’ Webinar, sponsored by the RCSB PDB. The webinar is based on our newly update, full length tutorial and will be presented next Wed. at 2 pm ET. You can register on the OpenHelix webinar page. [Jennifer]
  • RT @JChrisPires: X Prize: Build a Star Trek ‘tricorder’ and win $10m http://t.co/Vt8L63Ub via #science #technology #SciFi #Startrek #genome #bioinformatics [Mary]
  • RT @drgitlin: Will Gene Patents Derail the Next-Generation of Genetic Technologies?:  A Reassessment of the Evidence Suggests Not http://t.co/QdeiwmEp [Mary]
  • RT @m_m_campbell: A healthy marriage. Bringing human #genetics & functional #genomics together to improve #health. Great read http://t.co/AR0XZsXu @NatureNews [Mary]

RCSB PDB free webinar

I just wanted to give a heads up to our free webinar on the RCSB Protein Databank. It’s going to be next Wednesday, at 11am Pacific US time. (that’s 18:00 UTC). It’ll be about an hour, and did I say it’s free?

Seating is limited, so register early.

You can see our announcement here: http://blog.openhelix.eu/?p=11055

and you can go register right now here: http://www.openhelix.com/cgi/webinars.cgi

If you can’t make the webinar, you can check out our training materials and tutorial here (also free, sponsored by RCSB PDB)

Video Tips of the Week: Annual Review IV (first half of 2011)

As you may know, we’ve been doing these video tips-of-the-week for FOUR years now. We have completed around 200 little tidbit introductions to various resources. At the end of the year we’ve established a sort of holiday tradition: 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.

You can see past years’ tips here: 2008 I, 2008 II, 2009 I, 2009 II, 2010 I, 2010 II. The summary of the second half of 2011 will be available next week here.

January 2011

January 5: SKIPPY predicting variants w/ splicing effects

January 12: Twitter in Bioinformatics. This one was much more popular than I expected!

January 19: PolyPhen, for predicting the possible effects of mutations in genes

January 26: iRefWeb + protein interaction curation

February 2011

February 2: RCSB PDB Data Distribution Summaries

February 9: SIFT, Sorting (SNPs) Intolerant From Tolerant another tool for predicting the impact of mutations in genes.

February 16: Melina II for promoter analysis

February 23: SNPTips and viewing personal genome data This tip is one of the most-watched ones we’ve had. Thousands of views on SciVee!

March 2011

March 2: DAnCER for disease-annotated epigenetics data

March 9: World Tour of Genomics Resources

March 16: Encyclopedia of Life

March 23: ORegAnno for regulatory annotation

March 30: MetaPhoOrs, orthology and paralogy predictions

April 2011

April 6: The Taverna Project for workflows

April 13: VirusMINT , the branch of the Molecular Interaction database for viral interactions

April 20: LAMHDI for animal models

April 27: Dot Plots, Synteny at VISTA

May 2011

May 4: MycoCosm

May 11: InterMine for mining “big data”

May 18: Allen Institute’s Brain Explorer

May 25: SciVee, the YouTube of science

June 2011

June 1: New and Improved OMIM®

June 8: Converting Genome Coordinates

June 15: MutaDATABASE, a centralized and standardized DNA variation database

June 22: Update to NCBI’s Cn3D Viewer

June 29: Orphanet for Rare Disease information

RapiData 2012, a course on Data Collection and Structure Solving

Hi folks–just got this notice from the PDB mailing list, thought I’d pass it along as a public service announcement:

We are offering RapiData 2012, the fourteenth offering of our popular

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/.
Students could be at any level from advanced undergraduate to full
professor. The course should accommodate 48 students total. We encourage
all students to bring their own specimens for data collection, and to
bring old data for the data-reduction and structure-solving tutorials.

Please read the Course Announcement at http://www.bnl.gov/RapiData/.
You’ll see that many experts in the field will be available for lectures
and tutorials. You’ll find the application materials on the Course
Application tab at this site.

For the tenth time we will hold a short lecture course on the fundamentals
of crystallography for roughly five hours on Sunday 22 April. The body of
the RapiData course really requires that students have a healthy knowledge
of crystallography. For potential students who have some experience but
are shaky about fundamentals, this course will help. There will be a small
additional fee for the fundamentals course, to pay for Saturday night
accomodations and food on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and
subsistence costs for Latin-American students and junior faculty (under 40
yrs). Please apply for the course, and then contact R. Sweet
(sweet@bnl.gov) if you are interested in applying for a scholarship.

In accordance with the standards of the International Union of
Crystallography, we observe the basic policy of non-discrimination,
affirming the right and freedom of scientists to associate in
international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race,
colour, language, age, or gender, in accordance with the Statutes of the
International Council for Science. At this course no barriers will exist
beyond the application procedure that would prevent the participation of
bona fide scientists.

Please apply or send your students to our course,

Bob Sweet, Sonya Kiss, and Alex Soares

Course Announcement at http://www.bnl.gov/RapiData/


Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Quick Reference Cards for teaching and outreach

We know there are a number of different ways that scientists and students become familiar with genomics software.   Some of it comes from the traditional publication routes–like the very handy NAR Database issue.  Or like the Current Protocols papers we’ve done recently.  We have these online tutorials that people use in various ways: some teach themselves by watching the video and working the exercises, some download the matching slide sets and run local workshops (our catalog: some are free/sponsored and green icons indicate that; red indicates subscription required). Librarians are using them to become “embedded” in courses in some cases.

A less-well-known type of material we have is the Quick Reference Card.  These are printed cards with URLs, hints, tips, definitions, shortcuts–for stuff that you may want a quick reminder of: where a feature is located, or how to use it.  People who run the local workshops will sometimes write to us to get a set for their courses.  They are great to give out at conferences to raise awareness of the software.

We have these cards for several resources that we also have free sponsored training videos + slides + exercises with: UCSC Genome Browser (2 cards–intro and table browser); Galaxy, and our newest: RCSB PDB and SGKB.  You can go to this form and order them, and we’ll send them out.

I bring this up today because we just received word from Ensembl that they have created a card that we can distribute as a PDF.  You can print it up and put it on the wall near the computer as a handy reminder of some features and tools at Ensembl.  Click the image to download the PDF, or go directly to the link below.


Order OpenHelix printed cards for resources: http://www.openhelix.com/cgi/qrcOrder.cgi

Ensembl PDF card download: Ensembl_card_march2010.pdf

Just an FYI: RCSB PDB has announced the release of our free PDB tutorial

Hey, just wanted to let you know that our updated tutorial on the RCSB PDB is now free, as announced by the RCSB PDB on Tuesday:

“Comprehensive training materials to introduce users to the features and functionality of the RCSB PDB are now freely available at openhelix.com.

The new training tools 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 resources and tools available at the RCSB PDB for research and education. The full tutorial runs for about an hour, and can be navigated by specific chapters.

The animated PowerPoint slides used as a basis for the tutorial can be downloaded, along with slide handouts, and exercises. These materials are freely available for teachers and professors to create classroom content…”

I’m sure that I am biased, but I think this tutorial is great & will help anyone use the RCSB PDB more efficiently. Check it out & be sure to let us know what you think of it, when you get a chance!

Tip of the Week: PSI SGKB’s Monthly Structural Genomics Update (Edited)

In today’s tip I’d like to show you the monthly Structural Genomics Update from the Protein Structure Initiative  Structural Genomics Knowledgebase or PSI SGKB. Some of you may not be aware of the PSI SGKB, but it is a resource related to the RCSB PDB resource, which is very well known. We are currently creating a tutorial that will feature the whole knowledgebase & we will be sure to let you know when that is available. Today I want to feature their monthly Structural Genomics Update, which provides a great collection of articles and features related to structural genomics and protein biology as a whole. The Update is produced by Nature Publishing Group in collaboration with the Protein Structure Initiative.

I cannot begin to cover the full functionality of the SGKB in this tip, so go over there & explore it, watch for our tutorial to come out, maybe even add an SGKB widget (Trey talked about it here) to your web site!  Also, feel free to let me know what your favorite part of the PSI SGKB is, when you get a chance. Enjoy the tip!

EDIT: If you tried to watch this tip yesterday & had trouble, it was not on your end. Apparently there was some glitch part way through during my upload (thanks for the heads up, Greg!). I’ve reloaded the movie file & it plays through now, so please try it again – this is a great resource that should not be missed!

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!