SBGrid Newsletter: August 2025

Dear Consortium Members and Affiliates,

As we cling to the waning days of summer here in Boston, we have our regular bevy of updates to share with ROCKET as our first software webinar of the season, a software push with 27 updates and four new titles, four new members to welcome, and two publication highlights.

Our monthly software webinars will resume in October with Alisia Fadini and Minhuan Li covering AlphaFold as a Prior: Guiding Protein Structure Prediction Using Experimental Data with ROCKET. 

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

Oct 14: Alisia Fadini and Minhuan Li - ROCKET 
Nov 11: Hui Wang - TomoNet

Stay tuned for additional dates

April 14: Jose Luis Vilas - scipionTomo

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 inclues updates to ACPyPE, AlphaPulldown, Boltz, CCP-EM, ChimeraX, CryoDRGN, Doppio, fpocket,  Geneious, Gnuplot, ISOLDE, IsoNet, MDAnalysis, MemBrain-seg, Napari, NMRFx-Analyst, NMRFx-Structure, pytom-matchpick, PyRosetta, RDKit, qFit, TomoDRGN, Topaz, VST, VST, warp, and XDS along with four new titles: CryoNeRF, E3-CryoFold, Napari-filaments, and Unicycler.

See Software Changes below for complete details.

Four new members joined in the month of August: Jeffrey Dvorin from Boston Children's Hospital, Dvir Harris from Technion - Israel Institute of Technology, Jiankun Lyu from Rockefeller University, and Weiwei Wang from UT Southwestern Medical Center. 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 Nature Communications publication from SBGrid member David Eliezer's lab out of the Weill Cornell Medicine that shows aggregated structures caused by key mutations in mitochondrial proteins that cause heretable versions of neurodegeneration. Read more: https://medium.com/sbgrid-community-news/structural-insights-into-rare-heritable-neurodegeneration-4af8bf1984dc

- Meharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a Nature Structural & Molecular Biology publication from the laboratory of Chi-Min Ho of Columbia University and colleagues who used cryo-electron tomography to map malaria’s ribosomes at work and reveal how a parasite-specific drug derails translation. Read more: https://medium.com/sbgrid-community-news/stopping-ribosomes-in-action-101e95f41784

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 11 new citations since our last reporting, from these SBGrid members: 

Goran Bajic from Icahn School of Medicine at Mount Sinai in Cell Reports: Clonotype-enriched somatic hypermutations drive affinity maturation of a public human antibody targeting an occluded sarbecovirus epitope; Seth Darst of Rockefeller University in Nature Communications: Real-time capture of σN transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding; Catherine Drennan from MIT in PNAS: Structural basis for anaerobic alkane activation by a multisubunit glycyl radical enzyme; Eric Fischer from Dana Farber Cancer Institute in Molecular Cell: Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation; Oriana Fisher from Wesleyan University in Journal of Biological Chemistry: Copper acquisition in Bacillus subtilis involves Cu(II) exchange between YcnI and YcnJ; Christopher Garcia from Stanford University School of Medicine in Science: De novo design and structure of a peptide-centric TCR mimic binding module; Davie Heppner from The State University of New York at Buffalo in Journal of Meicinal Chemistry: Profiling and Optimizing Targeted Covalent Inhibitors through EGFR-Guided Studies; Borden Lacy from Vanderbilt University Medical Center in Infection and Immunity: Mouse monoclonal antibodies against Clostridioides difficile toxins TcdA and TcdB target diverse epitopes for neutralization; Jason McLellan from The University of Texas at Austin in Journal of Experimental Medicine: Repertoire, function, and structure of serological antibodies induced by the R21/Matrix-M malaria vaccine; Carsten Sachse of Forschungszentrum Jülich in PNAS: The bacterial ESCRT-III PspA rods thin lipid tubules and increase membrane curvature through helix α0 interactions; and Joost Snijder from Utrecht University in ACS Infectious Diseases: Structural Basis for Postfusion-Specific Binding to the Respiratory Syncytial Virus F Protein by the Canonical Antigenic Site I Antibody 131–2a.

CryoNeRF is a computational tool for homogeneous and heterogeneous (conformational and compositional) cryo-EM reconstruction in Euclidean 3D space:

https://github.com/UNITES-Lab/CryoNeRF.

E3-CryoFold 5e9385a is a deep learning framework for automating the determination of three-dimensional atomic structures from high-resolution Cryo-EM density maps. It addresses the limitations of existing AI-based methods by providing an end-to-end solution that integrates training and inference into a single streamlined pipeline. E3-CryoFold combines 3D and sequence Transformers for feature extraction and employs an equivariant graph neural network to build accurate atomic structures from density maps: https://github.com/A4Bio/E3-CryoFold#e3-cryofold-end-to-end-prediction-for-cryo-em-structure-determinationupdated. 

Napari-filaments 0.4.0 is a napari plugin for filament analysis. This plugin helps you manually track filaments using path shapes of Shapes layer and was added to napari 0.6.4 for Linux: https://github.com/hanjinliu/napari-filaments.

Unicycler 0.5.1 is an assembly pipeline for bacterial genomes that assembles Illumina-only read sets where it functions as a SPAdes-optimizer. It can also assemble long-read-only sets (PacBio or Nanopore), where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a short-read-first hybrid assembly: https://github.com/rrwick/Unicycler.

ACPyPE 2023.10.27 is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with other python applications like CCPN and ARIA. It also now uses AmberTools 23.3: https://github.com/alanwilter/acpype/releases/tag/2023.10.27 

AlphaPulldown 2.0.4 includes updates to the modelcif converter for compatibility with the latest modelcif version, improved documentation with specific jax version requirements and updated uniref30 URLs, and enhanced random seed generation based on the backend in use. The release also fixes filtering criteria handling for multimeric templates and adds new tests for monomeric and multimeric feature dictionaries: https://github.com/KosinskiLab/AlphaPulldown/releases/tag/2.0.4.

Boltz 2.2.0 includes fixes for contact and pocket conditioning functionality that was not fully operational in Boltz2, along with new potentials and optional kernels to avoid installation issues on non-Linux platforms. This release also adds new security features for MSA server usage and includes numerous bug fixes and performance improvements: https://github.com/jwohlwend/boltz/releases/tag/v2.2.0.

CCP-EM 20221108 is now available.

ChimeraX 1.10.1 includes enhanced command line search functionality that allows typed text to be found anywhere in the command using the Alt/Option key, trajectory analysis improvements with RMSD and hydrogen bond plotting capabilities, and a new Thermal Ellipsoids GUI tool for displaying atomic anisotropic B-factors. This update also introduces Boltz 2 structure prediction with affinity prediction capabilities and an improved ViewDock interface: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog.

CryoDRGN 3.5.0 introduces 1-indexing for output epochs and volumes to improve the user experience, adds a new beta autodecoder training command that omits the encoder for faster runtimes, and includes enhanced landscape analysis with Leiden clustering. This release also adds support for parsing RELION5 tomography files, automatic analysis execution after training completion, and expands compatibility to Python 3.12: https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.5.0

Doppio 1.3.0 includes new jobs for the full RELION 5 sub-tomogram averaging pipeline, EulerMate, ProSMART and MetalCoord, updates in visualization of outputs for LocScale, Model Validation, and Fetch from AlphaFold DB jobs in Coot and ChimeraX, and other jobs options. It adds an interactive image viewer to allow browsing of images and volumes in job results and to run custom scripts when launching Coot, Chimera, or ChimeraX, and updates EMDB and EMPIAR deposition features and validation of job running options, along with minor bug fixes and updates:

https://www.ccpem.ac.uk/docs/doppio/release_notes.html.

fpocket 4.2.2 fixes bugs in atom_site parsing and chain reading for atoms in read_mmcif, along with improvements to descriptor output functionality: https://github.com/Discngine/fpocket/releases/tag/4.2.2.

Geneious 2025.2 includes new features and enhancements in Gibson and InFusion cloning, primer extensions, and cloud workspace. Also new are usability improvements in streamlined UI, workflows, and cloning validation along with minor fixes and changes: https://assets.geneious.com/documentation/geneious/release_notes.html#v2025.2.

Gnuplot 6.0.3 contains several new features (in contourfill, plot, save changes among others) and improvements (in 3D polygon objects, hsteps, win) back-ported from the

development version, together with minor bug-fixes: https://sourceforge.net/projects/gnuplot/files/gnuplot/6.0.3/RELEASE_NOTES_6_0_3/download.

ISOLDE 1.10.1 is a minor bugfix release that relaxes the ChimeraX version requirement back to 1.10.0 and fixes a harmless but annoying traceback that occurred on first install: https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde?platform=Linux&version=1.10.

IsoNet 0.3 is a maintenance release that fixes many bugs and has been tested with TensorFlow 2.5. The spIsoNet denoising functionality was verified on tomograms, though users should note the package requires an older TensorFlow version due to compatibility issues with newer releases: https://github.com/IsoNet-cryoET/IsoNet/releases/tag/v0.3.

MDAnalysis 2.9.0 adds support for Gromacs 2024.4 and 2025 TPR files, introduces a new "water" keyword for selecting water residues, and switches from fasteners to filelock dependency. This release includes parallel analysis support for nucleic acids, contacts, and density modules, enhanced XYZ writer precision control, and moves several analysis modules (hole2, psa, waterdynamics) to optional mdakits dependencies that will be completely removed in v3.0: https://github.com/MDAnalysis/mdanalysis/releases/tag/package-2.9.0.

MemBrain-seg 0.0.9 includes fixes for pixel size documentation issues, padding functionality, and enables CPU device support for skeletonization. This release also adds spectral rescaling through padding and cropping, fixes annotation padding with ignore labels, and updates documentation to include the latest segmentation model:

https://github.com/teamtomo/membrain-seg/releases/tag/v0.0.9.

Napari 0.6.4 adds an option to run scripts from the command line and adjusts the napari console toggle to place focus on the console, and fixes a number of bugs: https://github.com/napari/napari/releases.

NMRFx-Analyst 11.4.26 is now available. 

NMRFx-Structure 11.4.26 was also updated.

pytom-match-pick 0.10.0 drops Python 3.10 support and adds Relion 5 compatibility through the new --relion5-compat flag for merge_stars. This version also includes enhanced testing for correlation functions and mask creation utilities:  https://github.com/SBC-Utrecht/pytom-match-pick/releases/tag/0.10.0.

PyRosetta 2025.33 includes recent Rosetta updates. Since functionality comes directly from the underlying Rosetta source code, new features available in Rosetta's 2025 developments—including recent AI integrations and updates to various algorithms—can be accessed via the PyRosetta interface: https://www.pyrosetta.org/home

RDKit 2025.03.5 includes support for clearPropertyCache() on ROMol and Atom objects, enhanced ChemDraw document support with read/write capabilities, and improved SMARTS parsing with error position reporting. This release fixes several critical issues including stereochemistry loss in minilib fragmentation, atom map number information loss with CXSMILES, and memory issues with RascalMCES:

https://github.com/rdkit/rdkit/releases/tag/Release_2025_03_5.

qFit 2025.2 introduces major architectural changes with CCTBX backend integration for file handling and transformer architecture, support for multi-model ensemble PDB inputs, and a new metric comparison pipeline for evaluating structural models against MTZ or CCP4 maps at both global and local levels:  https://github.com/ExcitedStates/qfit-3.0/releases/tag/2025.2.

TomoDRGN 1.0.1 fixes a critical bug in starfile.py that prevented nextPYP users from using filter_star.py in their workflow. This update adds support for processing the tomodrgn_preprocessed.star file generated during train_vae, resolving indexing errors that were blocking integration with nextPYP pipelines:  https://github.com/bpowell122/tomodrgn/releases/tag/v1.0.1.

Topaz 0.3.13 is now available.

VST 0.10.0 is a major code refactor that now supports datasets larger than system memory, which is possible by converting datasets to zarr format and loading only the required chunks when needed, enabling efficient processing of larger-scale data:  https://github.com/fgdfgfthgr-fox/Volume_Seg_Tool/releases/tag/v0.10.0.

VST 0.10.1 was also pushed out.

Warp v2.0.0dev35 includes a number of bug fixes and updates:

https://github.com/warpem/warp/compare/v2.0.0dev34...v2.0.0dev35

 XDS 20250714 includes changes to background determination to improve untrusted pixel detection; spatial correction tables not required for INIT.

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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