Newsletter

Dear Consortium Members and Affiliates,

As we look ahead to the new academic season we have the latest round of SBGrid news to share, with a resumption of our monthly software webinar series, a software push with 6 updates and 4 new tools, a welcome for 4 new members, progress on a new benchmarking project, and 3 member publication highlights.

Our monthly Software Webinar Series will return in the fall. We have a trio of new software titles to introduce you to with our first three webinars: Assembline, an assembly line of macromolecular assemblies; Proteus, a general purpose program for protein design; and TomoTwin-cryoet, for particle picking in Tomograms using triplet networks and metric learning. We'll be adding more speakers to the lineup below, so please be sure to let us know if there is a topic or software title you'd like to hear more about. You can find a library of our past webinars on the SBGrid YouTube channel.

For our August software push you'll find updates to AlphaFold, AreTomo, PyMOL, Rosetta, samtools, and Schrödinger, along with 4 new titles:  CryoCARE, MemBrain, Surface Morphometrics toolkit, and TomoTwin. See Software Changes below for complete details.

Four new members joined in the month of August:  Sarah Shahmoradian from UT Southwestern Medical Center, Bassem Al-Sady from University of California, San Francisco, Altos Labs, and Seismic Therapeutic. Welcome to our newest members!

Technical notes from our Software Team

Wiki Update: Recommended Hardware and Benchmarking

Thanks to our summer student from Grinnell College - Cynthia Hu - who benchmarked reference cryo-em datasets across a range of systems at HMS and on AWS. We've added these new benchmarking results to our wiki (https://sbgrid.org//wiki/recommended) as an initial effort to provide guidance across a range of software, datasets, and hardware configurations that may inform future purchasing decisions. Please contact us with feedback or interest in participating in this project.

Member Publications Highlights

Over 100 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:

SBGrid citations: SBGrid's eLife paper received 12 new citations in the month of August, from these SBGrid members:

Titus Boggon from Yale University in Nature Communications:

SH3 domain regulation of RhoGAP activity: Crosstalk between p120RasGAP and DLC1 RhoGAP; Bing Chen from Boston Children’s Hospital, in Science Immunology: An Antibody from Single Human VH-rearranging Mouse Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion; Brandt Eichman from Vanderbilt University in Journal of Biological Chemistry: The SOS response-associated peptidase (SRAP) domain of YedK catalyzes ring opening of abasic sites and reversal of its DNA–protein cross-link;

Katrina Forest from University of Wisconsin-Madison in Acta Crystallographica Section D: The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases; Ryan Hibbs from University of Texas Southwestern Medical Center in Nature Communications: Structural and dynamic mechanisms of GABAA receptor modulators with opposing activities; Lynne Howell from The Hospital for Sick Children in PLOS Pathogens: The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing; Jean-Philippe Julien from The Hospital for Sick Children Research Institute in Immunity: Vaccination with a structure-based stabilized version of malarial antigen Pfs48/45 elicits ultra-potent transmission-blocking antibody responses; Jason McLellan from University of Texas, Austin in Cell Reports: Structural basis for non-canonical integrin engagement by Bordetella adenylate cyclase toxin; Ohad Medalila from University of Zurich in eLife: An amphipathic helix in Brl1 is required for nuclear pore complex biogenesis in S. cerevisiae;

Ignacio Mir-Sanchis from Umeå University in Nucleic Acids Research: Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility; Shaun Rawson from the Harvard Cryo-Electron Microscopy Center for Structural Biology in Nature Structural and Molecular Biology: Yeast PI31 inhibits the proteasome by a direct multisite mechanism; and Sichen Shao from Harvard Medical School in Nature Structural and Molecular Biology: Mechanism of client selection by the protein quality-control factor UBE2O

Software Changes

AlphaFold v2.2.3 is a bug fix release.

AreTomo 1.2.5 includes an optimized, parallel implementation of the local alignment that can save ~ 30% processing time with patch alignment enabled and a bug fix for generating the flipped volume.

cryoCARE is new to SBGrid at version 0.1.1. cryoCARE (Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data) dramatically increases contrast in cryo-TEM images, which improves the interpretability of the acquired data. This package is the

memory-efficient implementation of cryoCARE.

MemBrain 767b477 is also new to the collection. MemBrain is a pipeline for automated detection of membrane-bound proteins in cryo-electron tomograms utilizing the geometry of a pre-segmented membrane to reduce the complexity of the detection task.

PyMOL 2.5.3 is a maintenance release.

Rosetta 3.13 includes a number of new features with a rejuvenation of the scientific benchmarking system, the availability of trRosetta in C++ Rosetta now, support for the new Mac M1, RosettaSurf, a surface-centric computational design approach, and many other changes outlined in the release notes.

SAMTools 1.16 is now available and includes a new reference command to extract the embedded reference from a CRAM file, UMI/barcode handling in samtools markdup, a  new template coordinate sort order in samtools sort and samtools merge, an update to the dict command to read BWA's .alt file and add AH:* tags indicating reference sequences that represent alternate loci, an option for the index command to accept multiple alignment filenames with the new -M option, and a new samtools fastq -T "*" that allows all tags from SAM records to be written to fastq headers, a counterpart to samtools import -T "*".

Schrödinger 2022-3 includes new FEP+ Groups to organize ligands with different states (protomers, tautomers, conformers), speed improvements for preparing high-quality protein structures for physics-based modeling, expanded application of residue scanning to explore up to 150,000 mutants in a single calculation, improved atom styling for large collections.

Surface Morphometrics Toolkit version 0.2 is new to SBGrid. The Surface Morphometrics Toolkit is a pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes using the Screened Poisson algorithm, calculate morphological features including curvature and membrane-membrane distance using pycurv's vector voting framework, and tools to convert these morphological quantities into morphometric insights.

TomoTwin 20220422_997b2a9 is the last new title for August. TomoTwin is a simple digital twin for synchrotron tomography that provides an API to generate realistic grayscale tomography datasets from ground-truth (labeled) volumes as training data for denoising and segmentation models.

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 https://sbgrid.org

Report software bugs: sbgrid.org/bugs