Dear Consortium Members and Affiliates,
It's time for the September SBGrid roundup. Read on for a profile on SBGrid member Gerhard Wagner, technical tips for overriding the default versions in our software stack, details on our rescheduled Phenix/DivCon webinar, a software push with 5 updates and 2 new titles, new open positions in SBGrid member labs, and three member publication highlights.
We caught up with Gerhard Wagner at Harvard Medical School for our September member tale. A pioneer in developing NMR techniques that revealed proteins behaving in unexpected ways, today Wagner sees new potential for NMR in visualizing protein-RNA complexes, while also focusing on translating tools developed for NMR to the world of cryoEM. Read the full story.
Tech tip for the month: version overrides. Did you know that we maintain at least 3 versions for most titles in your SBGrid installation? If you need to reproduce results from an experiment using a previous version, running sbgrid -l will give you a list of available versions. Find the version you need and place an override file named .sbgrid.conf in your $HOME directory designating the desired version (see our wiki for a detailed example) to override the default. And if you don't see the version you need on the list, let us know. We have many older versions available in our archive.
We had a bit of a technology snafu at our September webinar, so the presentation from Lance Westerhoff on Phenix/DivCon, has been rescheduled for Oct 2. Join us on Tuesday to hear about XModeScore: using crystallography to determine protonation states, fragment binding modes, and flip-states. Details here.
Our September software update includes new versions of BioXTAS RAW, CCP4, crYOLO, RELION, and Schrodinger, and two new software title: DENSS and pdb-tools.
Check our position postings page for the latest open positions in SBGrid member labs, currently featuring postings for postdoctoral fellows in Alexandra Deaconescu's group at Brown University and a Senior Scientist in Cryo-Electron Microscopy in Antonina Roll-Mecak's NIH laboratory. Learn more.
September brought us 2 new members: Charles Weitz from Harvard Medical School and Jonathan Shu from Cornell. 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 was cited in six recent publications, with a nod from La Trobe's Marc Kvansakul in Cell Death and Disease [Abstract]; Andrew McCarthy at EMBL Grenoble in Molecular Cell [Abstract], Katya Heldwein at Tufts in Journal of Biological Chemistry [Abstract], Vanderbilt's Terunaga Nakagawa in Journal of Biological Chemistry [Abstract], Utrecht University's Alexandre Bonvin in Journal of Computer-Aided Molecular Design [Abstract], and James Holton from UCSF in BioRxiv [Abstract].
Forty member publications appeared in journals this month. You can find a complete listing on our website, along with a few notable highlights below:
- CRISPR superstar Jennifer Doudna of UC Berkeley has a new publication in Science, presenting her group's discovery of natural CRISPR-Cas12a inhibitors, which before have been elusive. [Abstract]
- Appearing in PNAS this month is a paper authored by Daved Fremont of Washington University in St. Louis examining the structural components involved in murine norovirus binding of bile acids and the CD300lf receptor. The study determined that bile acid strengthened MNoV cell-binding and infectivity, suggesting a possible new target for treatment of the stomach flu. [Abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose a Journal of Immunology paper from Christopher Garcia's laboratory, in which they used structure-guided design to engineer a covalently linked IL-2 cytokine/antibody fusion to enhance targeting of IL-2 to T regulatory cells. [Abstract].
BioXTAS RAW version 1.5.0 was pushed out. With this update, RAW is now compatible with wxpython4, now uses the numba just-in-time compiler instead of weave, was updated to incorporate the new DENSS alignment code, and now saves configuration files in JSON format (note: earlier versions of RAW will not be able to open configuration files created with version 1.5.0 or later; however configuration files created in earlier versions of RAW are compatible with version 1.5.0).
CCP4 version 7.0.062 includes a major overhaul of monomers, a new EM reference structure in buccaneer, updates to dials, xia2, ccp4i2, and morda, and the addition of Molprobity from the Richardson lab.
DENSS is a new addition to SBGrid. DENsity from Solution Scattering (DENSS) is an algorithm used for calculating ab initio electron density maps directly from solution scattering data. DENSS implements a novel iterative structure factor retrieval algorithm to cycle between real space density and reciprocal space structure factors, applying appropriate restraints in each domain to obtain a set of structure factors whose intensities are consistent with experimental data and whose electron density is consistent with expected real space properties of particles.
RELION 3.0_beta was updated with the latest changes.
Schrodinger's quarter release 2018-3 is now available. This quarterly release includes new features and performance enhancements across all of our software. New tutorials are also available on Schrodinger's Training Page, covering enumeration tools, defining QM and MM regions in QSites, and A Chemist's Guide to Maestro Materials Science.
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.