SBGrid Consortium - News and Events

Newsletter for November 2022

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Published November 2022

Dear Consortium Members and Affiliates,

Here at SBGrid, we're just catching up from the Thanksgiving holiday and sending along this monthly update before we blink and the year is through. Read on for an the latest on our webinar series, a profile on SBGrid member Eva Nogales, a BIG software push with 19 updates and 5 new titles, 3 new members to welcome, some changes to Linux requirements, a reminder to give our Software Installation Manager a try, and 3 member publication highlights. Whew!

Our first two webinars of the season are now posted to online; check out introductions to two new tools in the collection: TomoTwin-cryoet and Assembline. Up next: Dec 13th - Proteus - a general purpose program for protein design, to redesign entire proteins or functional sites such as ligand-binding pocket. Prof. Thomas Simonson from Ecole Polytechnique and the Centre National de la Recherche Scientifique will present.

Upcoming SBGrid Webinars

Dec 13: Prof. Thomas Simonson - Proteus

Jan 10: Chris Waudby, Ph.D.- TITAN: Getting the most from NMR titration experiments with two-dimensional lineshape analysis

Feb 14, SPECIAL TIME - 10am EST: Prof. Martin Steinegger - Fast and accurate protein structure search with Foldseek

Mar 14: Kiarash Jamali, Ph.D. - ModelAngelo: Automated atomic model building for cryo-EM

Apr 11: Gustaf Ahdritz - OpenFold

May 9: TBD

Jun 13: Prof. Woonghee Lee - POKY

Webinar registration and details here

For this month's SBGrid Tale, we caught up with Eva Nogales at University of California, Berkeley, who's been at the cryoEM thing since the early days with a long-time focus on microtubules, and who credits her success to the power of human connection, from the high school teachers who gave her early inspiration to the team that surrounds her in the lab, giving and getting the energy to make that next discovery together. [Read the full story].

Our November software push is a big one, with updates to Anaconda, AreTomo, APBS, ATSAS, AWS CLI, Blast+, CCP4, cryoDRGN, DIALS, FASTA, Geneious, IMOD, ModelAngelo, NModeller10.4eggia, ProDy, RDKit, SIDESPLITTER, and starfile, along with five new titles: RFDesign, TtomoTwin-cryoet, POKY, OmegaFold, and Vina-GPU. See Software Changes below for complete details.

Three new members joined in November: Dawanna White and Graham Chakafana from Hampton University and Jeffrey Lee from University of Toronto. Welcome to our newest members!

Looking ahead to December, the SBGrid team and Harvard Medical School will be on winter break starting December 22nd through January 2. Be sure to contact us earlier in December if you have questions or need additional support.

Technical notes from our Software Team

SBGrid Linux requirements: We recently updated the list of requirements for running SBGrid on Linux to include libxcb, which provides an interface to the X Window System protocol. Many packages require this library and it is probably already present on most systems. For more info on required packages, see https://sbgrid.org//wiki/workstation_setup#packages-for-rhel-7-and-8-and-compatible-machines

SBGrid Installation Manager: If you haven't already, you may want to give the SBGrid Installation Manger a whirl. This very popular tool is available for Mac and Linux in GUI and command line flavors and allows users to cherry-pick a few applications from the SBGrid collection or install the whole shabang. Users in SBGrid member labs can register for an account at www.sbgrid.org/registration/register/ and use those credentials to install the software on any desktop, laptop, or cloud resources where you use the software. Email us at bugs@sbgrid.org with any questions.

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:

•

Peng Yuan of Washington University School of Medicine, Saint Louis describes the use cryo-EM to investigate the potassium-dependent mechanosensitive MscK channel and its activation pathway in a new Nature Communications publication. Results uncovered a curved transmembrane domain (TMD) in the heptameric channel that flattens and expands upon channel opening that could be the mechanotransduction mechanism.

[Abstract]

•	A new paper in The EMBO Journal from the lab of Kevin Corbett at the University of California, San Diego reveals a two-protein transcriptional regulator team, consisting of CapH and CapP, that triggers bacterial CBASS immune system response to DNA damage. [Abstract]

•

From our graduate student desk, Harvard student Kristen Rodrigues highlighted a Science publication from Anna Pyle's laboratory at Yale University in which the authors shed light on the mechanistic basis of group IIC bacterial intron retrotransposon formation using cryoEM to visualize intact group IIC intron-maturase retroelement. [Read more].

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:

Structural biology applications used in this project were compiled and configured by SBGrid [1].

[1] 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 citations: SBGrid's eLife paper received 9 new citations in the month of November, in publication including these SBGrid member laboratories:

Titus Boggon of Yale University in Structure: Tandem engagement of phosphotyrosines by the dual SH2 domains of p120RasGAP; Alexandre Bonvin of University Utrecht in Nature Communications: PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation; Stephen Burley of Rutgers in Protein Science: RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D; Christopher Fromme of Cornell University in Structure: Structure of the RhlR-PqsE complex from Pseudomonas aeruginosa reveals mechanistic insights into quorum-sensing gene regulation; Eric Lee of University of Ottawa in Data in Brief: Data on structural analysis of cholesterol binding and sterol selectivity by ABCG5/G8; Roderick MacKinnon of The Rockefeller University in Neuron: Structural and functional analyses of a GPCR-inhibited ion channel TRPM3; Cristina Paulino University of Groningen in eLife:

Inhibited KdpFABC transitions into an E1 off-cycle state; Frank Sicheri of University of Toronto in Structure: Crystal structure of the CDK11 kinase domain bound to the small-molecule inhibitor OTS964; Feng Zhang of MIT in Science: RNA-activated protein cleavage with a CRISPR-associated endopeptidase

Software Changes

Anaconda version 2022.10 is out and includes updates to Conda (v22.9.0) and Anaconda Navigator (v2.3.1), a python-3.10 variant for anaconda metapackages (note: python-3.7 will not be provided after this release), and Qt support for macOS M1 (osx-arm64), enabling full use of GUI applications like Anaconda Navigator and Spyder.

AreTomo is now at release 1.3.2.

APBS was updated to 3.4.1

ATSAS 3.1.3 is the new default.

AWS CLI is now at version 2.0.24.

Blast+ 2.13.0 includes new SRA BLAST programs, ARM Linux executables, and an option to produce database metadata along with other improvements and bug fixes.

cryoDRGN was bumped to release 1.1.2.

DIALS 3.12 is the new default.

fasta 36.3.8i includes updates /get_protein.py and annotation scripts, fixes to remove duplicate variant annotations and to reduce mktemp compilation warning messages, and changes to annotation scripts for Pfam shutdown: new ann_pfam_www.py, ann_pfam_sql.py.

Geneious 2022.2.2 includes a few fixes, including a bug that caused a cloning operation to reset custom annotation colors, a failure to install Doench 2016 algorithm in CRISPR, a bug that prevented importing fastq files into Shared and Geneious Server Databases, and a bug that prevented copying folders.

IMOD 4.11.21 is available, see the changelog for details.

OmegaFold is the first of our new titles. OmegaFold enables high-resolution de novo structure prediction from a single primary sequence.

ModelAngelo is now at 0.2.2.

Modeller was updated to 10.4, which includes minor updates to eliminate the 3-character limit to residue names when reading from or writing to mmCIF files, add Python 3.11 support, and fix the modXXX compatibility script on macOS 13 (Ventura) on Apple Silicon (M1/ARM64) Macs.

Neggia 1.2.0 adds support for Data Layout Message version 4 and new tools for checking HDF5 compatibility along with a few bug fixes.

POKY version 20220805 is now in the SBGrid collection. POKY is a software suite for multidimensional NMR, 3D structure calculation of biomolecules.

ProDy was bumped to 2.3.1. New features since 2.3 include a Gamma function class from GOdMD and a prody energy app based on ClustENM.

RDKit 2022.09.1 includes a new RegistrationHash module used to build a registration system with the RDKit. Also new is an initial version of a C++ implementation of the xyz2mol algorithm for assigning bonds and bond orders based on atomic positions, and new functionality in minimallib accessible from JavaScript and other programming languages.

RFDesign is new to the SBGrid collection at version c882ab0. RFDesign is used for protein hallucination and inpainting with RoseTTAFold

SIDESPLITTER was updated to release 1.2.

starfile version 0.4.11 is out.

TomoTwin-cryoet 0.2.0 is another new SBGrid title. TomoTwin-cryoet is used for particle picking in Tomograms using triplet networks and metric learning. Check out this recent webinar to learn more about this new tool.

Vina-GPU is new addition number five. Vina-GPU is a heterogeneous OpenCL implementation of AutoDock Vina for accelerating.

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

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