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Dear Consortium Members and Affiliates,
We zipped right through April and here again with our monthly update, with a thank you to all who participated in our recent webinar series, our monthly tale featuring New Zealand PI Kurt Krause, a software push with updates to 8 applications and 3 new titles, 2 new members to welcome, a position posting from the Harvard Cryo-EM center for Structural Biology, and 2 member publication highlights.
We closed out the SBGrid Spring Webinar Series with a final talk on Tuesday and are grateful to all of the speakers who participated over the last seven weeks, and to you all for attending and making this series a success! Stay tuned for our next round of webinars in the coming weeks. Many of our hosted webinars are posted to the SBGrid YouTube channel. |
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For our April SBGrid Tale, we crossed a few time zones to connect with Kurt Krause for whom fist fights, evening chats with The Colonel, glow worms, and a "let's give it a go" philosophy lit his path to Otago, New Zealand. As a physician-scientist, Krause leads a laboratory focused on the structural biology of infectious diseases where he shines a light on the proteins and enzymes involved in diseases like tuberculosis and coronavirus and on the biology of bioluminescence. [Read the full story]
Our software push for April includes updates to 8 applications - Alphafold, ALBULA, ChimeraX, Geneious, pyrosetta, SamTools, scipion, and Schrodinger - along with the addition of three new titles: AreTomo, Icebreaker, and Emap2sec+. See Software Changes below for complete details.
Two new members joined in April: Josefina del Mármol from Harvard Medical School and Kymera Therapeutics. Welcome to our newest members!
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Community Announcements |
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CryoET Specialist - Harvard Medical School The Harvard Cryo-EM center for Structural biology is seeking a CryoET specialist to join our team to support and expand investigations of cellular and macromolecular structures. https://cryoem.hms.harvard.edu/cryoet-specialist-job-opening
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Member Publications Highlights |
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Over 75 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple of notable highlights below:
Deposit your experimental datasets: If you're currently preparing a manuscript, please remember that, while you're making the PDB record deposit and publication submission, you can also preserve your primary experimental datasets with deposits to the SBGrid Data Bank.
Acknowledge SBGrid: SBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.
Please use this SBGrid logo on the acknowledgements slide of your presentations.
We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software: |
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SBGrid citations: SBGrid's eLife paper received 5 new citations in the month of April, from these SBGrid-member laboratories: Jennifer Bridwell-Rabb from University of Michigan in Nature Communications Biology: Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT; Mike Eck from Dana-Farber Cancer Institute in Nature Cancer: An allosteric inhibitor against the therapy-resistant mutant forms of EGFR in non-small cell lung cancer; Robert Landick from University of Wisconsin–Madison in Nature: Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile; James Letts from University of California, Davis in Science: Structures of Tetrahymena’s respiratory chain reveal the diversity of eukaryotic core metabolism; Marc Kvansakul from La Trobe University in Viruses: Structural Insight into KsBcl-2 Mediated Apoptosis Inhibition by Kaposi Sarcoma Associated Herpes Virus.
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Software Changes |
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ALBULA was updated to version 4.0.
AreTomo was added to the SBGrid collection at version 1.1.0. AreTomo (Alignment and Reconstruction for Electron Tomography) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.
ChimeraX nightly build fixes a bug that sets occupancy & bfactors to zero when saving pdbs.
Emap2sec+ is new to SBGrid. Emap2sec+ uses deep learning to accurately identify structures, alpha helices, beta sheets, other(coils/turns), and DNA/RNA in CryoEM maps of medium to low resolution.
Geneious is at version 2022.1.1, which includes the latest patch as well as the 2022.1 update with new options to scale up your cloning throughput with Parts Cloning, perform Golden Gate cloning in batch using sequence lists, stop Golden Gate cloning operations one by one, and import easily import and characterize primer databases stored in excel.
Icebreaker is another title new to SBGrid. At version 0.3.5, Icebreaker is used for ice gradient estimation and removal on cryoEM micrographs.
PyRosetta is now at release 2022.12.
SAMtools 1.15.1 is a bug fix release.
Schrodinger 2022-1 was pushed out.
Scipion was updated to 3.0.10.
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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.
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More information about the SBGrid Consortium is available at https://sbgrid.org Report software bugs: sbgrid.org/bugs
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