SBGrid Newsletter: March 2025

Dear Consortium Members and Affiliates,

The first days of spring have brought some much needed light to these dark days, and with renewed vigor we write with the latest SBGrid news, including a profile of SBGrid member Ryan Hibbs, details on the upcoming Warp software webinar, a software push with thirteen updates and seven new titles, four new members to welcome, and two member publication highlights. 

Our April member tale puts the spotlight on Ryan Hibbs from University of California, San Diego, who has learned to make the most of surprises, both personally and professionally. Hibbs's work on ion channels is divided between between synapse and sinew, examining how neurotransmitter receptors function in muscle and in the mind. [Read More] 

Join us April 8th for a software webinar with Alister Burt from Genentech sharing the latest on Warp. If you missed our March webinar on DeepMainmast and DAQ, you can listen to the recorded version with Genki Terashi presenting on the SBGrid YouTube channel.

To receive email reminders about upcoming webinars, please be sure to register for the series! Registration here: https://sbgrid.org/webinars/#register

Apr 8: Dimitry Tegunov - Warp

May 13: Ellen Zhong - DRGN-AI

June 10:  Genki Terashi - DiffModeler & CryoREAD: Macromolecular and Nucleic Acid Structure Modeling for Cryo-EM Maps Using Deep Learning

Webinar registration and details

SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Meharry Medical College.

This month's software push includes updates to 3D Slicer, AreTomo3, ATSAS, BindCraft, ChimeraX, Doppio, DAQ Score, EMAN2, Geneious, Hole, MDAnalysis, VMD, and Warp, along with seven new titles: MPicker, Protenix, RECOVAR, smap, Tomotools, Volume_Seg_Tool, and warp-tm-vis. See Software Changes below for complete details.

Four new members joined in the month of February: Chris Brown from University of Otago, Aravindan Ilangovan from Queen Mary University of London, Chrystal Starbird from University of North Carolina Chapel Hill, and Alexandra Trkola from University of Zurich. Welcome to our newest members!

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:

- Caltech doctoral student Vida Storm Robertson highlighted a publication in Acta Cryst F, from SBGrid member Craig Smith at Washington University in St Louis School of Medicine and colleagues, that shows the first structure of a crucial enzyme for nucleotide synthesis and lays the foundation for future drug development efforts. [Read more]

- Meharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a publication from the laboratory of SBGrid member Jeffrey Holt and colleagues that appeared in Hearing Research and demonstrates that TMC1 and TMC2, previously known as key components of mechanotransduction channels in auditory hair cells, also function as essential lipid scramblases required for phosphatidylserine externalization, linking sensory transduction to membrane homeostasis in the ear. [Read more]

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.

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's eLife paper received four new citations since our last reporting, from these SBGrid members: 

Daniel Hurdiss from Utrecht University in Journal of Nanobiotechnology: A bivalent spike-targeting nanobody with anti-sarbecovirus activity; Andrew Kruse from Harvard Medical School in PNAS: Epitope-directed selection of GPCR nanobody ligands with evolvable function; Sichen Shao from Harvard Medical School in Nature Communications: Mechanism of ASF1 engagement by CDAN1; and Niraj Tolia at National Institutes of Health in Cell Reports Medicine: A strain-transcending anti-AMA1 human monoclonal antibody neutralizes malaria parasites independent of direct RON2L receptor blockade.

We added seven new titles to the SBGrid collection this month, including:

MPicker 1.2.0 is a tool for membrane flattening and visualization in cryo-electron tomography, enabling researchers to effectively analyze membrane proteins by transforming curved membrane surfaces into flat representations for improved structural interpretation and particle picking. Learn more: https://thuem.net/software/mpicker/overview.html.

Protenix 0.4.4 is a trainable PyTorch reproduction of AlphaFold 3. Learn more: https://github.com/bytedance/Protenix.

RECOVAR, at version 20250226, is a software tool for analyzing different conformations in heterogeneous cryo-EM and cryo-ET datasets. RECOVAR can reconstruct high-resolution volumes, estimate conformational density and low free-energy motions, and automatically identify subsets of images with a particular volume feature. Learn more: https://github.com/ma-gilles/recovar?tab=readme-ov-file.

smap 2.1 is used for detecting unlabeled macromolecules in 2D Cryo-EM images of cells using high-resolution template matching. Learn more: https://github.com/jpr-smap/smap_v2.1.

tomotools 0.4.3 provides a collection of scripts designed to make cryo-electron tomography a bit easier. Learn more: https://github.com/tomotools/tomotools.

Volume_Seg_Tool 20250128 is used for 3D volumetric electron microscopy image segmentation, enabling both semantic and instance segmentation of grayscale volumetric data with high efficiency and accuracy. Learn more: https://github.com/fgdfgfthgr-fox/Volume_Seg_Tool

warp-tm-vis version 0.0.1 is a tool that visualizes template matching results from Warp, allows for changes between different tomograms, turning on/off visualization of tomograms, correlation volumes, and particle positions, and simulation of thresholding results at a given cutoff. Learn more: https://github.com/warpem/warp-tm-vis.

Updates were pushed for another thirteen applications:

3D Slicer 5.8.1 introduces new interactive tools, improved shadows, a DICOM browser, and a revamped training portal. It also adds over 20 extensions and enhances core modules with better performance and usability. Release notes: https://discourse.slicer.org/t/slicer-5-8-summary-highlights-and-changelog/41988. 

AreTomo3 was updated to release 2.1.0, which introduces improvements to tilt axis finding and motion correction code. Release notes:

https://github.com/czimaginginstitute/AreTomo3/blob/main/Readme.txt.

ATSAS is now at version 4.0.1. ATSAS 4 includes a few new programs: a launcher for all subprograms, efamix, mixtures, and peak/qt. The GUI was also completely redesigned and many other improvements and features have been added. Release notes: https://biosaxs-com.github.io/atsas/4.0.0/. 

BindCraft 1.5.0 is the new default. This new release fixes some critical bugs, improves the default design settings, and adds new options for complex re-prediction for hard targets. Additional details at https://github.com/martinpacesa/BindCraft/releases.

ChimeraX 20250305 is available via version override and includes MUSCLE v5, LAMMPS trajectory support, improved residue labeling, and sequence manipulation tools. Release notes: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog.

DAQ Score was updated to release 1.1.0 with updates to dependencies in requirements.txt and optimized Makefiles, an updated readme, and torch version to 2.6.0. Release notes: https://github.com/kiharalab/DAQ/releases.

Doppio 1.2.0rc provides various bug fixes and enhancements. Release notes: https://www.ccpem.ac.uk/docs/doppio/release_notes.html

EMAN2 was updated to 2.99.66. In this release GPUs are used for neural network tasks like tomogram annotation and particle picking, offering significant speed improvements, with current developments based on TensorFlow.

Geneious version 2025.1 is out and introduces native Apple Silicon support, enhanced cloning validation, and improved Cloud Workspace functionality. Release notes: https://assets.geneious.com/documentation/geneious/release_notes.html.

Hole 2.3.1 brings improved control of buildsystem and compiler options. Release notes: https://github.com/osmart/hole2/releases.

MDAnalysis was updated to version 2.8.0 and includes improved topology guessing, parallelization support for various analysis tools, and relicensing to LGPLv3+.  Release notes: https://github.com/MDAnalysis/mdanalysis/releases.

VMD 2.0 is an alpha release and is now available for Linux. This release is part of a major overhaul and introduces a new interface, advanced rendering, and faster calculations. The developers note that updates are planned throughout 2025 with plans for a revamped plugin system and enhanced usability. Release notes: https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD.

Warp 2.0.0dev32 is the latest developer release. It includes minor bug fixes.

https://github.com/warpem/warp/compare/v2.0.0dev32...main.

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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