Dear Consortium Members and Affiliates,
Summer is upon us along with the lure of lazy days at the beach, but the SBGrid team has the usual round of updates to pass along, including info on how to find us at the Toronto ACA meeting in July, a story on EMBL Heidelberg group leader Orsolya Barabas, a link to our recent webinar and a preview of what's to come, a software update with two new titles and three updates, two new members to welcome, and three member publication highlights.
Catch us at ACA 2018 in Toronto! We are poster SA26 in Poster Session 1 on July 21. Drop by to talk structural biology computing or just to say hello. And if you'd like a 30-minute one-on-one with Jason Key, our technical lead, email us to set up a time.
For our June member tale Orsolya Barabas from EMBL, Heidelberg is in the spotlight. Transposons have been the subject of her studies for over a decade, with projects focused on accelerating and limiting their activity, to supercharge immune cells and fight antibiotic resistance. Read the full story.
You can find our latest webinar recording on "Using Scipion for Stream Image Processing at Cryo-EM Facilities" on the SBGrid YouTube Channel. Thanks to José Miguel de la Rosa Trevin for joining us to present. We're working on our fall lineup of webinars now, so please let us know if you'd like to hear more about a particular software title. Here's a glimps of what's to come:
- Sept 25: EVcouplings with Debora Marks
- Dec 4: PanDDA with Nick Pearce
- Nov 6: Relion 3.0 with Sjors Scheres
For our June software release we pushed out updates to 3 titles - OpenBabel, IMOD, and Qt - along with 2 new titles: cryoEF and THUNDER.
June brought us two new members, Colin Garvey from the Broad Institute and Daniel Leahy at the University of Texas at Austin. Welcome to our newest members!
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 SBGrid Data Bank 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.
SBGrid's eLife paper got 6 new citations in June, with nods from Jonathan Sheehan from Vanderbilt Center for Structural Biology [Abstract], Andrew Kruse of Harvard Medical School [Abstract], Jean-Phillipe Julien at the University of Toronto [Abstract], Chris Garcia of Stanford University [Abstract], Eric Fischer from Dana-Farber Cancer Institute [Abstract], and Sebastien Granier at the Institut Génomique Fonctionnellle [Abstract].
More than 45 member publications appeared in journals this month. You can find a complete listing on our website, along with a few notable highlights below:
- In the Journal of Biological Chemistry, University of Massachusetts Medical School's Celia Schiffer and William Royer investigate the importance of the tetramer in C-terminal binding protein 1 and 2 (CtBP1 and CtBP2) function. [Abstract].
- William Weis of Stanford University coauthors a paper in the Annual Review of Biochemistry detailing the molecular pathway of G protein–coupled receptor (GPCR) activation. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues chose a new Nature publication co-authored by SBGrid member Oliver Ernst, in which the authors utilize cryoEM to visualize the structure of rhodopsin in complex with Gi (inhibitory)-coupled receptors [More on Tumblr].
cryoEF, at version 1.1.0, is new to SBGrid. CryoEF is an open-source software package for robust analysis of the orientation distribution of cryoelectron microscopy data.
IMOD was updated to development version 4.10.14, available via version override. You can find a full list of changes in the IMOD History file.
OpenBabel is now at version 2.4.1, a release that represents a major update. Key features include integration of the confab conformer generator, improved partial charge models (including EEM methods, EQeq), ECFP radial fingerprints, initial support for ring rotamer / conformer sampling, improved GAFF atom typing and parameterization, new PHP scripting bindings, and many new file formats, features and bug fixes.
Qt 5.9.6 includes 33 bug fixes and many other improvements.
THUNDER is another new SBGrid title at version 1.3.5. THUNDER is a particle-filter framework for robust cryoEM 3D reconstruction.
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.