I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (
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I love using molecular structures as teaching tools. They're beautiful, they're easy to obtain, and working with them is fun.
But working with molecular structures as an educators can present some challenges. The biggest problem is that many of the articles describing the structures are not accessible, particularly those published by the ACS (American Chemical Society). I'm hoping that the new NIH Open Access policy will include legacy publications and increase access to lots of publications about structures.
It would also be great if other funding agencies, like the National Science Foundation, would follow suit and require their grantees to make articles open access as well.
When I wrote the "Exploring DNA Structures" lab manual, I also made a CD with lots of structures that served as "unknowns." This was intentional, on my part, because I thought the unknowns would make good research projects for students. The students could follow the links to the structure and read (or skim) the publication to find out what the structure was supposed to show and what hypothesis the authors were trying to test.
After the manual was published though, I heard from some college instructors asking me if I could tell them what the structures were and what they did. I spent a lot of time working to answer those questions and ended up compiling several pages of information about those structures in the instructor guide. In doing so, I also learned that many of the papers weren't accessible. Students at some universities might have access, but not students at community colleges or high schools.
I finally ended up including a table to show which structures were accompanied by accessible articles so that teachers would know which ones were safe to assign to their students.
I don't know how many structural studies are funded by the NIH, and how many are funded by other agencies like the NSF, but I'm sure looking forward to increased access, being able to read more papers, and to assign more of them to students without worrying about whether or not they'll have access.
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For macromolecules, and until more articles are available, you could use the advanced search tool in the PDB (http://www.pdb.org/pdb/search/advSearch.do, way at the bottom under citations) and query structures for journals that are totally free. JBC alone has over 4000 over a year old (free)-it would seem like you could instruct students to search in these journals: http://highwire.stanford.edu/lists/freeart.dtl, and find a structure they like.
Posted by: RobertC | April 8, 2008 3:07 PM
Thanks Robert,
That sounds like a good idea. and I agree, JBC is great!
Posted by: Sandra Porter | April 8, 2008 3:15 PM
Almost makes you wish that providing a PDF of the publication describing the structure should be required by the PDB ....
Posted by: Ron | April 8, 2008 3:55 PM
That idea could backfire. I don't know about the PDB, but I know that some databases have a hard time getting people to submit their results. You certainly don't want to make that part of the process any harder.
Funding agencies, unlike database, have some leverage. They can hold people accountable and make them do the right thing.
Posted by: Sandra Porter | April 8, 2008 3:59 PM
Funding agencies would have to drive the process, that's for sure. Not being a crystallographer, are they required to deposit coordinates by NIH or NSF?
Also, did you chance to see this:
http://aminopop.com/wordpress/?p=170
(sent you the round-about way). It would be extremely cool to have lots of models to hand out when talking about structures. Bet they cost an arm and a leg now.
Posted by: Ron | April 8, 2008 4:26 PM
I'm not sure about NIH or NSF requiring it, but every journal I've ever published in requires deposition of coordinates. Its pretty unheard of not to deposit coordinates, and recently, most people are depositing structure factors. As for PDFs-the PDB links to PUBMED abstracts, which link to pubmed central, free text, etc. For example,
http://www.pdb.org/pdb/explore.do?structureId=1JY2
click on the 'M' and you'll get the paper. I forgot to mention that besides JBC, PNAS would provide a lot of great structures with free papers....
Posted by: RobertC | April 8, 2008 5:21 PM
I'm not sure about NIH or NSF requiring it, but every journal I've ever published in requires deposition of coordinates. Its pretty unheard of not to deposit coordinates, and recently, most people are depositing structure factors. As for PDFs-the PDB links to PUBMED abstracts, which link to pubmed central, free text, etc. For example,
http://www.pdb.org/pdb/explore.do?structureId=1JY2
click on the 'M' and you'll get the paper. I forgot to mention that besides JBC, PNAS would provide a lot of great structures with free papers....
Posted by: RobertC | April 8, 2008 5:24 PM
Both the PDB and the NCBI's structure databases link to the abstracts for articles describing the structures and some of them are free (JBC, NAR, Nature, and some others)
But there are many articles that I would like to see that are not freely available.
The journal Biochemistry, for example, charges $25 an article.
That's why I'm looking forward to open access.
Posted by: Sandra Porter | April 8, 2008 5:38 PM
I was pretty sure that the journals required deposition, but wasn't absolutely sure. :-)
I wish more journals would allow free access to their on-line content after X number of months (with X=12 being the maximum). Nature and Science being two large holdouts (at least last I checked). Granted, they may have some contractual obligations to sort out before they can move to free content. Still, it would be nice...
Posted by: Ron | April 8, 2008 8:05 PM
Apologies for coming late to this discussion.
A colleague showed me this article, and it inspired me to create a list of all those structures in the PDB that currently have an 'Open Access' publication associated as the primary citation. I did this using queries to PubMed Central.
You can find the results of my investigation archived on the PDBWiki website here:
http://pdbwiki.org/index.php/Free_text
PDBWiki is an open experiment in user contributed annotation of the macromolecular structures in the PDB.
It would be really great if you would consider contributing or linking some of your educational resources to PDBWiki.
Posted by: Dan Bolser | April 15, 2008 8:57 AM
PDBWiki is very nice Dan! I will certainly link to it when I update my blogroll.
Posted by: Sandra Porter | April 15, 2008 1:56 PM