SBGrid Newsletter: November 2019
Dear Consortium Members and Affiliates,
Before you head out for the holiday weekend, catch up on the latest SBGrid news, with a temporary fix for SBGrid - Mac Catalina woes, links to watch and connect to our latest webinars, a software push with 7 updates and 5 new titles, 3 new members to welcome, and 3 member publication highlights.
If you're looking to buy a new Mac or update to MacOS 10.15 Catalina, please note that Catalina is not currently compatible with SBGrid. We're working on a permanent solution, so our first recommendation is that you hold off upgrading for a bit longer. If you've already upgraded or have a new machine on the way, we do have this work-around to get SBGrid up and going.
In last week's webinar we hosted Steven Ludtke, who presented the latest from EMAN2, including a complete tomography pipeline and in situ structural biology. Watch on the SBGrid YouTube channel. In December we'll hear about the automatic 2D class selection application - Cinderella - from Thorsten Wagner. [Webinar details here].
Our November software push includes updates to these seven titles: ATSAS, crYOLO, FFmpeg, Modeller, MotionCor2, PHENIX, and Rosetta. We've also added 5 new electron tomography applications from the laboratory of Jose-Jesus Fernandez: TOMOAND, TOMOBFLOWd, TOMOCTF, TOMOSEGMEM, and TOMO3D. See Software Changes below for complete details.
Three new members joined during the last month: Sandra Gabelli from Johns Hopkins School of Medicine, Robert Kirchdoerfer of the University of Wisconsin-Madison, and Aaron Gregory Schmidt from Massachusetts General Hospital. Welcome to our newest members!
Over 50 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:
A new publication from Lynne Howell of the University of Toronto appears in Nature Communications, focusing on identifying the relevance of multiple conformations in guiding PilT function in the type IV pilus-like systems, which are essential for virulence in many bacterial species. Abstract
In Antibodies, Charles Craik of the University of California, San Francisco, has a new paper unveiling antibody-drug conjugates (ADCs) targeting the urokinase receptor (uPAR) as a potentially viable treatment of triple negative breast cancer (TNBC). Abstract
From our graduate student desk, Harvard student Kristen Rodrigues highlighted a publication, to which SBGrid member James Fraser contributed a structure, that appeared in Science this month and describes a computational method to design a synthetic protein sense-and-response system that scientists can generalize. Read more
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.
SBGrid's eLife paper received 5 new citations in the month of November, from Sandra Gabelli's group at Johns Hopkins University in the Journal of Biological Chemistry: An engineered antibody fragment targeting mutant β-catenin via Major Histocompatibility Complex I neoantigen presentation; the Protein Data Bank in Europe in a new Nucleic Acids Research publication: PDBe: improved findability of macromolecular structure data in the PDB; Borden Lacy's laboratory at Vanderbilt University appearing in Nature Microbiology: Structural insights into the transition of Clostridioides difficile binary toxin from prepore to pore; the laboratory of Alexandre Bonvin at Utrecht University in the journal Structure: Modeling Antibody-Antigen Complexes by Information-Driven Docking, and from software contributor Tristan Bepler of Bonnie Berger's laboratory at MIT in BioRxiv: Topaz-Denoise: general deep denoising models for cryoEM.
ATSAS was bumped to version 3.0.0-3. 3.0 is a major new release with improvements to pre_bunch, crysol and crysol 3.0, crysol 3.0:dattools, damesv/monsa, gasbori/gasborp/gasbormx, pdbtools (pdb2seq, pdbstat, seqstat), primus/qt, and saspy. A host of new tools were also added to this suite: cif2pdb for converting mmcif files to pdb format; damemb to generate cubic search volume for membrane proteins; elllip for an ellipsoidal model of a liposome; bilmix for modelling polydisperse unilamellar lipid vesicles with asymmetric density profiles; lipmix to model polydisperse unilamellar/multilamellar lipid vesicles; datmif for ab initio modelling directly to experimental SAS data, without p(r); datresample to statistically correct resampling of experimental data frames; nmator for normal mode analysis in torsion-angle space; imsim to simulate 2D scattering data from calculated scattering intensity from crysol (.abs); im2dat for radial averaging of 2D images to 1D scattering patterns; imop performs image operations similar to datop, and flexbin to do quaternary structure modelling of a dimeric complex formed by flexible subunits.
BioXTAS RAW was bumped to version 1.6.3, which fixes a critical bug when averaging files.
crYOLO version 1.5.3 is out and is mostly a bug fix release.
ffmpeg version 4.2.1, known as "Ada" is now available. With the bump to 4.2 users will notice a number of changes, detailed thoroughly on the ffmpeg change log.
MotionCor2 1.3.0 is the new default.
PHENIX 1.17.1-3660 was pushed out, and includes improved handling of SHELX data in phenix.reflection_file_converter, new options to output eLBOW files to Amber, eLBOW support for the QM package Orca, updated map smoothing, and a fix to the inconsistency in clashscore values in phenix.validation_cryoem when hydrogens are in the model.
Rosetta was updated to version 3.11.
Modeller version 9.23 is the new default. This release includes added support for Python 3.8, improvements to model.read(), which now allows chain IDs longer than one in model_segment when reading mmCIF files, and can now understand mmCIF format author-provided chain IDs, which are used instead of the canonical chain ID if available
TOMO... a collection of electron tomography titles from the lab of Jose-Jesus Fernandez is new to SBGrid:
• TOMOAND, for noise reduction with anisotrophic nonlinear diffusion. See the TOMOAND website. • TOMOBFLOW, for feature-preserving noice filtering. See the TOMOBFLOW website. • TOMOCTF for CTF determination and correction. TOMOCTF website. • TOMOSEGMEM for membrane segmentation. See the TOMOSEGMEM website. • TOMO3D for fast tomographic reconstruction on multicore computers. See the TOMO3D website. 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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