SBGrid Newsletter: October 2026
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Dear Consortium Members and Affiliates,
Our October SBGrid news includes an update on the SBGrid CryoEM Tournament scheduled to wrap up in early November, a recording of our recent webinar on cryoCAT, a date for our next webinar on hax-em in Scipion, a software push with 13 updates and three new titles, two new members to welcome, PHP patching notes, upcoming events from our partners at Instruct-ERIC, two science tales from our student contributors that highlight recent member publications, and appreciation for those who remembered to cite SBGrid in their publications.
The SBGrid CryoEM Cloud Tournament is ongoing, bringing together 29 international teams to process the same confidential cryo-EM dataset in dedicated SBCloud environments. Registration is now closed, but the tournament will continue until November 6, with teams competing to produce a scientifically supported reconstruction at the lowest possible computational cost in fully open-source and combined/non-open-source software categories. Supported by AWS, the tournament will provide a community benchmark of cryo-EM workflow quality, reproducibility, and cost efficiency. We will announce the winner in each category in late November.
Beata Turoňová, Project Group Leader at Max Planck Institute of Biophysics, kicked off our software webinar series in October with an introduction to cryoCAT, Contextual Analysis Tools for cryo-ET. If you missed her presentation, the recording is now available on the SBGrid YouTube channel. Next up: From static maps to continuous motions: conformational variability analysis with hax-em in Scipion. Join us November 10 to hear from David Herreros, postdoctoral researcher from the Biocomputing Unit, Centro Nacional de Biotecnología.
To receive email reminders about upcoming webinars, please be sure to register for the series! Registration here: https://sbgrid.org/webinars/#register |
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November 10: David Herreros - From static maps to continuous motions: conformational variability analysis with hax-em in Scipion. December 8: Yousef Metwally - TomoTwin-cryoet
January 12: Marten Chaillet - miss-alignment February 9: Beata Turoňová - GAPSTOP(TM)
April 13: Lucrezia Catapano - Coot & Moorhen: evolving model building from desktop to web.
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. |
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This month's software push includes updates to 13 titles – Ais, Alphafold3, AlphaPulldown, BioXTAS RAW, cs2star, DOCK, DSSP, IMOD, NMRFx, OpenFreeEnergy, Pom, RDKit, and Volume_Seg_Tool – along with three new applications: CryoCodex, ESM, and EPU_group_AFIS_ratolonfork. See Software Changes below for complete details. Two new members joined in the month of October, both from Boston Children's Hospital: David Dowling and Jonathan Kagan. Welcome to our newest members! |
Technical Notes from our Software Team |
PHP Patch: Vulnerable PHP packages were removed from the SBGrid software collection. Please update your installation to receive the latest changes. |
Upcoming events from our partners at Instruct-ERIC |
Biochemistry Webinar: Lipid Interactions Driving Actinoporin Pore Architecture and Stoichiometry November 4, 2026 | 9-10am ET / 2-3pm GMT | Virtual
Speaker: Dr Gašper Šolinc, National Institute of Chemistry, Slovenia Chair: Dr Lindsay McDermott, University of Bedfordshire, UK
Register here: https://register.gotowebinar.com/register/8447683533179015515 Instruct-ERIC Webinar Series: Structure Meets Function Webinar 51
November 17, 2026 | 5am ET/11am CET Speaker: Antje Gohla, University of Würzburg: Generating tools to probe the antineoplastic roles of vitamin B6
Speaker: Josan Marquez, EMBL Grenoble: Talk title TBD Register here: https://events.teams.microsoft.com/event/678aac9a-5225-43a0-85dd-fda162f17d87@8bf65d25-a796-44ab-80d7-1e76c12247ad Building Molecular Systems for MD Training Nov 26-27, 2026 | University of Manchester, UK
A hands-on workshop in preparing biomolecular systems for molecular dynamics simulations Register here: https://instruct-eric.org/events/building-molecular-systems-for-md/
3rd European Congress on Mass Spectrometry and Analytical Techniques April 19-20, 2027 | Barcelona, Spain
Intelligent Mass Spectrometry: AI, Automation, and Advanced Analytics Details here: https://scisynopsisconferences.com/mass-spectrometry |
Member Publication Highlights |
Over 100 new member publications appeared in journals this month. You can find a listing on our website, along with a couple of notable highlights below: |
Student contributors highlight member publications with a focus on science education and demonstrating how structural biology and preclinical science connect to medicine.
- Fisk University student Cariuna Ellison's highlight features research appearing in PLOS Pathogens from Allison Didychuk's Yale University School of Medicine laboratory in which the authors describe their investigations into an accessory packaging protein to understand its specific role in herpesvirus replication and infection. [Learn more.]
- Lipscomb University student Vina Nguyen chose to highlight research from the laboratory of Anne Marie Wehenkel of Institut Pasteur that appeared in Science Advances and reports on the use of an AI to read images of treated bacteria to identify how a drug attacks them, which could speed up the process for developing new antibiotics for drug-resistant TB. [Learn more.]
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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: https://data.sbgrid.org/ |
SBGrid operations are primarily funded with member fees and grants, so we are grateful when you can acknowledge SBGrid in manuscripts, preprints, and related work where appropriate. We recommend the following language for inclusion in the methods section of your publications that report results obtained with SBGrid supported software: |
Software: Computational analyses were performed using the SBGrid software environment, which provides curated, version-controlled structural biology applications and reproducible execution environments across platforms (Herre et al., 2024).
Software and computational environment: All computational analyses were carried out using the SBGrid software environment, which provides curated, version-controlled access to structural biology software and manages dependencies to support reproducible research. Software execution was supported through the SBGrid Capsules framework, which standardizes application environments and workflows across platforms, as described in Herre et al. (2024).
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The following new titles were added to the SBGrid collection in October:
CryoCodex is a tool for cryo-EM density maps, estimating local map quality, and predicting molecular masks. It produces an enhanced map, local quality scores for both the original and enhanced maps, and a molecular mask to support map interpretation and structural analysis. It also offers a faster cropped-map processing mode and full-map processing. Available in SBGrid at version 1.0.0. https://github.com/YangLab-SDU/CryoCodex
EPU_group_AFIS_ratolonfork takes the XML metadata from an EPU session that used AFIS (Aberration Free Image Shift) for faster acquisition and organizes the collected micrograph movies into RELION Optics Groups. In RELION version 3.1, where these groups were introduced, they can be used to further reduce the effects of high-order aberrations on the data induced by using large amounts of beam-image shift. The output movies.star uses the RELION 5.0 STAR format (# version 50001), matching what relion_import writes. Version 0.2.1 is available in SBGrid.
https://github.com/ratolon/EPU_group_AFIS (code fork from https://github.com/DustinMorado/EPU_group_AFIS)
ESM is a protein modellng package providing ESMC, a protein language model trained on billions of sequences, and ESMFold2, which predicts all-atom protein structures from amino acid sequences with optional multiple sequence alignments. The models support protein sequence analysis, structure prediction, protein-complex modeling, and protein binder design, with pretrained weights available for local use. The version available in SBGrid is 3.4.1.post1.
https://github.com/Biohub/esm |
New releases or versions added for existing titles in the SBGrid collection are included below:
Ais 1.2.38 adds new 2D segmentation model options, including a Dice-only training variant, and improves model loading. It also removes a redundant 3D model variant and corrects architecture references in the documentation.
https://github.com/mgflast/Ais/releases/tag/v1.2.38
Alphafold3 was reclassified in the SBGrid collection to reflect a license change for the code from non-commercial to an open source Apache 2.0 license. All users can now access this tool, but are still required to apply for an download Alphafold3 models and databases directly from the developers. See our wiki for additional information: https://docs.sbgrid.org/apps/alphafold3/
AlphaPulldown 2.10.0 adds optional GPU-accelerated inference for AlphaFold 2-Multimer and AlphaFold 3, delivering approximately 2–2.7× faster AF2-Multimer predictions and up to 2× faster AF3 predictions on supported NVIDIA GPUs. A persistent JAX compilation cache reduces repeated compilation overhead, while bug fixes correct confidence scores for padded AF2 predictions, resolve GPU relaxation errors, and improve AF3 batch stability on network filesystems.
https://github.com/KosinskiLab/AlphaPulldown/releases/tag/2.10.0
BioXTAS RAW 2.4.2 fixes compatibility issues with older workspaces and settings files, improves reliability when loading and saving HDF5 workspaces, and resolves several problems with series data loading and processing. Prebuilt versions now include GPU support for image radial averaging across all operating systems, as well as multiprocessing support on macOS. https://sourceforge.net/p/bioxtasraw/news/2026/09/raw-242-released/
cs2star 0.7.0 is now available. https://github.com/brisvag/cs2star/releases/tag/v0.7.0
DOCK 6.13.1 fixes an issue with matching spheres and atoms during ligand orientation. The 6.13 series also adds frequency-based fragment and torsion selection in DOCK_DN, more flexible molecular weight filtering and improved mutation handling in DOCK_GA, optional ligand efficiency scoring, and greater control over the number of conformers retained during docking. https://github.com/docking-org/dock6/releases/tag/v6.13.1
DSSP 4.5.8 includes minor changes. https://github.com/PDB-REDO/dssp/releases/tag/v4.5.8
IMOD 5.1.13 is now available. https://bio3d.colorado.edu/imod/#Release%20Notes
NMRFx 12.0.8 improves the NMR analysis interface with new dataset and peak-list tabs, fixes disappearing toolbar icons, and improves peak-list updates. It also fixes issues when loading projects without molecular structures, improves error handling in the graphical matching tools, and adds a warning when updating the application with an active project. https://github.com/nanalysis/nmrfx/releases/tag/v12.0.8
OpenFreeEnergy 1.13.0 introduces experimental task-based execution for managing free energy calculation campaigns, adds user-defined Boresch restraints for SepTop and absolute binding free energy calculations, and provides automatic structural analysis for absolute binding and solvation protocols. It also improves convergence analysis, adds force-field-based partial charge assignment, and strengthens atom-mapping validation.
https://github.com/OpenFreeEnergy/openfe/releases/tag/v1.13.0
Pom 1.2.1 improves visualization of cellular cryo-electron tomography data with headless GPU rendering on Linux, allowing images to be generated without a graphical display and distributing work across multiple GPUs. It also corrects image proportions for non-square tomograms, produces sharper rotating 3D visualizations, and improves rendering performance and error reporting. https://github.com/mgflast/Pom/releases/tag/v1.2.1
RDKit 2026.09.1 introduces improvements to molecular conformer generation, including experimental ETKDGv4 and new coordinate embedding methods. It adds shape-based searching of synthon libraries, improves molecular substructure searching and tautomer canonicalization performance, and updates ring detection for greater speed and accuracy. Numerous bug fixes address stereochemistry, molecular drawing, file parsing, and force-field calculations.
https://github.com/rdkit/rdkit/releases/tag/Release_2026_09_1
Volume_Seg_Tool 0.13.3 improves memory efficiency and introduces a better cropping strategy for instance segmentation, and significantly speeds up instance segmentation metric calculations.
https://github.com/fgdfgfthgr-fox/Volume_Seg_Tool/releases/tag/v0.13.3 |
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. Learn more about SBGrid - Consortium website: https://sbgrid.org - Supported software: https://sbgrid.org/software/
- Report software bugs: sbgrid.org/bugs
This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium. |
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