Dear Consortium Members and Affiliates,
It's summer's last gasp for many of us who are returning to the school-year slog with kids or classes or teaching, so you're getting a slimmer version of our monthly update a few days early, as we breathe in those last days of freedom. We've still got news for you, with news on our webinar series, a small software push with updates to five titles, one new position posted from an SBGrid group, six new members to welcome, and two member publication highlights.
What's our most popular webinar? We took a look back at our collection and found this Introduction to Biological Small Angle Scattering presentation from Thomas Grant was the winner by far, with over 58,000 views, and viewership higher now than when it was first published. Looking ahead, we'll resume our webinar series on September 24th with a primer on ISOLDE, a tool for building high-quality macromolecular models into low-medium resolution experimental maps. Sept webinar details here.
A small software update will go out this month, with new versions of Bsoft, crYOLO, MAFFT, NMRPipe, and WebLogo. See Software Changes below for complete details.
We've updated our SBGrid member position postings page to include a new opening at the University of Wisconsin-Madison cryo-EM research facility for an Assistant Scientist who will support a new research facility with Krios, Arctica, Talos L120C, and Aquilos electron microscopes. See this and other postings here.
August brought us 6 new members, with Anthony Kossiakoff, Rama Ranganathan, and Minglei Zhao joining a large group of SBGrid PIS at the University Chicago, Yang Gao becoming our 4th member from Rice University, Robert Grant joining two other member PIs at MIT, and Breann Brown becoming our 18th member at Vanderbilt. Welcome to our newest members!
Member Publications Over 60 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:
• Published in an August issue of Molecular Biology of the Cell is a perspective by UCSF and Chan-Zuckerberg Biohub investigator, Adam Frost, comparing ancient and modern dynamin superfamily proteins to ascertain the mechanisms of their allosteric and membrane fission roles, as well as insights into how specific mutations can lead to disease states. Abstract
• In the Preview section of Molecular Cell, Yunsun Nam's group at UT Southwestern Medical Center examines two recent papers on m6Am modification that corroborate previous studies pointing to PCIF1 as the enzyme responsible for m6Am marks, provide a more accurate map of m6Am, and attempt to unravel the part m6Am plays in translation and gene expression. Abstract
If you're currently preparing a manuscript, please remember you can publish your datasets in the SBGrid Data Bank along with your PDB record deposit and publication submission to preserve your primary experimental datasets. We also recommend the following boilerplate language in all publications that report results obtained with SBGrid supported software:
Structural biology applications used in this project were compiled and configured by SBGrid .
 A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.
Link to article: https://elifesciences.org/articles/01456.
Four new citations popped up for SBGrid's eLife paper in August, with mentions from Alexandre Bonvin's lab at Utrecht University in a bioRxiv publication Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK; the laboratories of Cristina Paulino and Dirk Slotboom of University of Groningen in Nature Communications: A one-gate elevator mechanism for the human neutral amino acid transporter ASCT2; Christopher Garcia in a Journal of Biological Chemistry paper from his laboratory at Stanford University School of Medicine: A strategy for the selection of monovalent antibodies that span protein dimer interfaces; and Lynne Howell's group at University of Toronto in another Journal of Biological Chemistry publication: Ega3 from the fungal pathogen Aspergillus fumigatus is an endo-α-1,4-galactosaminidase that disrupts microbialbiofilms.
Bsoft version 2.0.5 is the new default.
crYOLO 1.4.1 is out. This update fixes the problem with long initialization times and includes a few other minor updates.
MAFFT version 7.429 fixes bugs in the --add, --merge, and --dash options.
NMRPIPE was updated to the latest version.
WebLogo version 3.7.1 is now available. With the bump to 3.7, the developers removed python 2.7 support, extended API documentation, changed the name of the python package from 'weblogolib' to 'weblogo', merged the 'corebio' package into 'weblogo', and made miscellaneous other minor bug fixes.
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.
This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium, the Structural Biology Grid computing consortium.
More information about the SBGrid Consortium is available at http://sbgrid.org
Report software bugs: sbgrid.org/bugs