SBGrid Newsletter: September 2026

Dear Consortium Members and Affiliates,

The SBGrid September update includes a story featuring software developer Shawn Zheng, instructions for requesting personal software installation credentials, details about our October webinar, a software push with 11 updates and two new titles, two new members to welcome, upcoming events from our partners at Instruct-ERIC, and two member publication highlights from our student contributors. 

Our September Tale features Shawn Zheng, whom you might find enjoying some fish and chips with his wife after a hike in the Bay Area, when he's not crafting solutions for cryoET experimentalists. At Biohub, Zheng's algorithm development team continues to develop AreTomoLive for reconstructing tomograms and data denoising, while casting an eye toward particle picking, the next data processing hurdle in the cryoET workflow. [Read More].

If you find yourself working through remote connections at home or while traveling, remember that SBGrid users can request personal credentials to install and maintain a subset of software on laptops or home workstations. This feature is free for all users in SBGrid member groups and ensures that you have access to the same software tools whether at home or in the lab. Request personal credentials.

October 13th at 12pm ET, Prof Beata Turoňová from Max Planck Institute of Biophysics will kick off our 2026-2027 software webinar series with an introduction to cryoCAT, a library of contextual analysis tools for cryo electron tomography and subtomogram averaging. Register here.

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

October 13: Beata Turoňová - cryoCAT

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.

This month's software push includes updates to 11 titles -- Amber, BindCraft, ChemEx, HTSlib, IMOD, NAMD, Octopi, Picard, PolNet, PowerFit, and Warp --  along with two new applications: Mosaic and PottsMPNN. 

See Software Changes below for complete details.

Two new members joined in the month of September: Sarah Doore from University of Florida and Craig Lindsley from Vanderbilt University.

Welcome to our newest members!

Structural Biology Meeting at Instruct-IT

October 20, 2026 | Florence, Italy

Details here: https://www.cerm.unifi.it/news/all-news/16-conferences/373-structural-biology-meeting-instruct-it

Scipion for Facilities Workshop 

Oct 29-30, 2026| Madrid, Spain

Organized in collaboration with National Center for Biotechnology (CNB)

Register here: https://i2pc.es/scipion-for-facilities-workshop-october-29-30-2026/

Instruct course on Virtual Drug Screening (VDS)

Nov 10-11, 2026 | Madrid, Spain

Organized in collaboration with National Center for Biotechnology (CNB)

Register here: https://i2pc.es/instruct-course-on-virtual-drug-screening-vds-madrid-november-2026/

Instruct.SI CryoEM Workshop 2026, Single Particle Analysis

Nov 10-12, 2026 | Ljubljana, Slovenia

Organized in collaboration with National Center for Biotechnology (CNB)

Registration deadline Oct 2: https://instruct-eric.si/spa2026/

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:

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 a publication in Nucleic Acids Research from Manuela Hospenthal and fellow researchers at ETH Zürich. They describes the molecular mechanisms behind bacterial natural transformation, revealing how bacteria import foreign genes and can lead to antibiotic resistance. [Learn more.]
• Lipscomb University student Vina Nguyen highlights work from the laboratory of Jonathan Abraham of Harvard Medical School and colleagues that appeared in Nature. Their research offers new insight into the monkeypox virus, for which there is still no treatment, revealing how its DNA-copying machine works and new possibilities for a first step toward developing therapies. [Learn 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:  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).

Reference: Herre C, Ho A, Eisenbraun B, et al. (2024). Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection. Acta Crystallographica D, 80. 

Link to article:https://journals.iucr.org/d/issues/2024/06/00/gm5107/index.html

SBGrid logo for use on the acknowledgements slide of presentations.

SBGrid's eLife and Acta Crystallographica D publications received 11 new citations since our last reporting, from these SBGrid members and contributing developers:

Goran Bajic from Icahn School of Medicine at Mount Sinai in Journal of Virology: Broadly reactive antibodies against influenza B virus hemagglutinin neutralize and protect through distinct structural mechanisms.

https://journals.asm.org/doi/full/10.1128/jvi.00802-26

Gira Bhabha from Johns Hopkins University in Journal of Biological Chemistry: Interactions of outer membrane lipoproteins Pseudomonas aeruginosa PA3214 and Escherichia coli PqiC with their MCE protein binding partners, PA3213 and PqiB.

https://www.jbc.org/article/S0021-9258(26)02358-6/fulltext  

Peter Dahlberg from SLAC National Accelerator Laboratory in ACS Nano: Cryo-Electron Tomography Reveals Nanoscale Thick Filament Disorganization in MYH7 P710R Hypertrophic Cardiomyopathy Cardiomyocytes.

https://pubs.acs.org/ancac3/article/20/34/23748/5272743/Cryo-Electron-Tomography-Reveals-Nanoscale-Thick

David Heppner from University at Buffalo in Angewandte Chemie International Edition: Thinking Outside the Binding Site: A Self-Encapsulating Kinase Inhibitor Remodels Its Pocket to Achieve Selectivity.

https://onlinelibrary.wiley.com/doi/full/10.1002/anie.2953141

Andrew Kruse from Harvard Medical School in Science Translational Medicine:  Multifunctional antibody responses from a primate Shigella outbreak inform vaccine design.

https://www.science.org/doi/abs/10.1126/scitranslmed.aef7084

The following new titles were added to the SBGrid collection:

Mosaic is a graphical tool for analyzing and modeling biological membranes from 3D structural data. It combines tomogram import, membrane segmentation, and surface meshing with protein localization and geometric measurements, and can export simulation-ready membrane systems for downstream molecular modeling and GROMACS workflows. Available at version 1.3.0.
https://github.com/KosinskiLab/mosaic

PottsMPNN is a protein design model for generating sequences from protein structures and predicting the energetic effects of mutations. It supports sequence optimization for stability and binding affinity, deep mutational scanning, and common ProteinMPNN-style design constraints, with workflows available through command-line scripts, Jupyter notebooks, and Google Colab. Available at version 1.1.0.

https://github.com/KeatingLab/PottsMPNN .

New releases or versions added for existing titles in the SBGrid collection are included below:

Amber 26 adds new capabilities for alchemical free-energy calculations, including optimized lambda scheduling, Boresch restraints, non-equilibrium work methods, and network-wide free-energy analysis. The release also introduces LIG-GaMD, a lignin force field, improved LEaP support for large systems, the ProPrep workflow manager, a GPU-accelerated tensor-based Poisson–Boltzmann solver, refined GBION parameters, and dSASA calculations for nonpolar solvation. AmberTools 26 further updates antechamber, RESP charge generation, cpptraj, and bundled LibTorch support. 

https://ambermd.org/AmberMD.php

BindCraft 1.5.3 includes small bug fixes to improve the reliability of the binder-design pipeline.

https://github.com/martinpacesa/BindCraft/releases

ChemEx 2026.09.1 includes several scientific corrections that can affect fitted parameters, simulated curves, uncertainties, residual weighting, and fit statistics, including changes to multi-state kinetic models and analyses involving binding, oligomerization, Eyring, very slow exchange, H/D exchange, duplicate uncertainties, and fitted profile scaling. It also adds new CPMG and ¹⁵N CEST tutorials and improves documentation of fitting and uncertainty handling.

https://github.com/gbouvignies/ChemEx/releases/tag/2026.09.1

HTSlib 1.24 removes experimental CRAM 4.0 support, adds faster parallel CRAM decoding, support for very long FASTA lines, multi-region iterators, and improved error checking, while fixing several security, stability, and indexing issues. 

https://github.com/samtools/htslib/releases/tag/1.24

IMOD 5.2.17 brings a broad set of tomography workflow improvements, including more robust patch tracking, the new Varypatchtrack workflow for optimizing patch-tracking parameters, and improved alignment of highly warped volumes. It also improves BatchRunTomo and Serieswatcher for cluster and remote-computer workflows, adds several 3dmod and Etomo usability improvements, and fixes numerous issues affecting alignment, reconstruction, CTF processing, snapshots, large images, and process management.
https://bio3d.colorado.edu/ftp/latestIMOD/recentChanges.txt

NAMD 3.0.3 fixes an incorrect wrapping bug in spinAngle in the Colvars in NAMD 3.0, 3.0.1 and 3.0.2. See announce.txt for details regarding correctness issues in: eABF and any other methods relying on extended Langrangian dynamics. This point release also fixes crashes in the GPU-offload GBIS simulations. 
https://www.ks.uiuc.edu/Research/namd/3.0.3/announce.html 

Octopi 1.7.0 adds multi-resolution training, sliding-window validation, Hugging Face support, and a URI-based command-line interface. It also fixes several localization issues, including centre-of-mass handling and data-portal pickling, and updates the CLI/API documentation and URI examples.

https://github.com/Biohub/octopi/releases/tag/octopi-v1.7.0

Picard 3.5.0 upgrades to HTSJDK 5.0.0 with CRAM 3.1 writing and faster BAM/CRAM I/O, and includes fixes for duplicate marking, fingerprinting, filtering, RNA-seq metrics, and SAM/BAM handling. SRA input support has been removed. 

https://github.com/broadinstitute/picard/releases/tag/3.5.0

PolNet 1.1.2 is a Python package for generating synthetic datasets of the cellular context for cryoET. In this new version execution is smoother, directly from the command line (without requiring Jupyter notebooks). It fixes the previous micrograph misalignment artifact shifted micrographs and no longer zero-fills the vacated edges, removing the black-border artifact that back-projected into reconstructed tomograms. https://github.com/anmartinezs/polnet/releases/tag/v1.1.2 

PowerFit 6.0.2 fixes minor bugs.

https://github.com/haddocking/powerfit/releases/tag/v6.0.2

Warp 2.0.0dev41 adds CUDA 12.9 support, CPU/GPU reconstruction, and Noise2Map training and inference. This release also fixes CPU reconstruction heap corruption after volume resizing, improves scalar half-precision conversion for rounding, subnormals, overflow, and NaN handling, and ensures command-line failures return nonzero exit codes.

https://github.com/warpem/warp/blob/main/CHANGES.md

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

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