Dear Consortium Members and Affiliates,
Our May update is a bit abbreviated, coming on the heels of the workshop we hosted last week. Still we have a few interesting tidbits to convey: a reminder about our upcoming webinar and a link to our May webinar recording, a software release with 2 updates and 2 new titles, and three highlights from member publications.
Last week we wrapped up Quo Vadis 2016, a two-day course on Advanced Data Collection and Model Building Techniques. Many thanks to our lecturers (Kay Diederichs, Paul Emsley, Wayne Hendrickson, James Holton, Jose Rodriguez, and Graeme Winter) and students, whose engagement and enthusiasm made for a productive workshop. We're hoping to host a workshop on Phasing using a similar hands-on format during the next year and would be glad to hear your suggestion for other topics.
Our June webinar features Ivet Bahar from the University of Pittsburgh giving an introduction to her software ProDy, a Python package for protein structural dynamics analysis. Please join us on the 21st - details here. You can also find a recording of Gunnar Schröder's presentation on DireX, the focus of our May webinar, on SBGrid's YouTube channel.
The monthly software release includes updates to CCP4 and Coot along with two new software applications: Gautomatch and Gctf.
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data in the Structural Biology Data Grid along with the PDB record deposit and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
For the month of May, SBGrid received 7 new citations in member publications: a paper in Proteins from Alexandre Bonvin's group at Utrecht University Proteins. 2016 May 12, a PNAS publication from Niraj Tolia's group at Washington University in St. Louis PNAS 2016 May 18, a story from Thomas Schwartz's group at MIT in PLOS PLoS Genet. 2016 May 3;12(5):e1006023, Olve Peersen's article in The Journal of Biological Chemistry from his group at Colorado State University J Biol Chem. 2016 May 2, a paper from Novartis and SBGrid member Enrico Malito in PLOS Pathogens PLoS Pathog. 2016 Apr;12:e1005557, a publication out of the University of Chicago and Sean Crosson's group in Nature Medicine Nat Med. 2016 May;22(5):563-7, and an article in Protein Science from Matthias Wolf's laboratory at the Okinawa Institute for Science and Technology Protein Sci. 2016;25:1147-55.
Over 70 publications from SBGrid member laboratories have appeared in journals since our last newsletter. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- A new Nature paper from the laboratory of Daniel Rosenbaum at the University of Texas Southwestern Medical Center presents the first atomic structure of the human sterol transporter complex ABCG5/ABCG8, offering insight into how these proteins work together to transport sterols across cell membranes. Read the full story.
- John Markley's group at the University of Wisconsin has developed a new algorithm to automate structure determination from NMR NOE data called AUDANA. Read their report in the Journal of Biomolecular NMR.
- From our undergraduate desk: Harvard student Kristen Rodrigues highlighted a new Nature paper from Peter Sorger's lab at Harvard Medical School that presents a new assay to measure how small molecule drugs effect cell division. Read more on Tumblr.
CCP4 version 7.0.014 is now available and includes a new release of refmac with updated scaling, new sharpeinging/blurring options for EM maps as well as crystallographic maps along with bug fixes and other new features. ARP/wARP was updated to work with the new refmac. Also included are fixes to the ccp4i2 coot interface, increased SF calculation speed in aimless, reading of anomalous maps in Coot, and multiple fixes in monomers.
Coot was updated to the latest pre-release, version 0.8.4-pre (Linux only).
Gautomatch version 0.5 (Linux only) was added to SBGrid. Gautomatch is a GPU-accelerated program for accurate, fast, flexible, and fully automatic particle picking from cryo-EM micrographs with or without templates.
Gctf version 0.5 (Linux only) is also new to SBGrid. Gctf is another GPU-accelerated program, this one for accurate and robust, real-time CTF determination of EM Micrographs.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.