SBGrid Newsletter: August 2026

Dear Consortium Members and Affiliates,

For our August SBGrid update have a profile on University of Otago scientist Mihnea Bostina, news on the launch of our CryoEM Cloud Tournament, a preview of the lineup for our software webinar series, a software push with 22 updates and one new title, four new members to welcome, a note from our technical team about anticipated macOS updates and changes to XDS licensing, upcoming event announcements from our partners at Instruct-ERIC, and three publication highlights from our student contributors. 

Our August Tale features Prof. Mihnea Bostina, who reflects on his scientific transit across the globe, moving from Bucharest to Frankfurt before stopping off in North America to study in Boston and Montreal, and finally making his home in New Zealand. From his laboratory at the University of Otago, Bostina's team works to burnish the reputation of often misunderstood viruses and harness their therapeutic potential, while also venturing into volume microscopy, a field where recent technical advances allow scientists to probe 3D structures of tissues, like cancer biopsies, more deeply. [Read more].

We're excited to launch the SBGrid CryoEM Cloud Tournament! Teams worldwide will analyze the same confidential, unpublished CryoEM dataset in a preconfigured AWS cloud environment, competing to deliver the most accurate, efficient, and scientifically useful results. The tournament is open to structural biologists, CryoEM researchers, developers, faculty, trainees, and research staff; SBGrid membership is not required. Complete this short, non-binding expression-of-interest form no later than September 8th to receive further details and learn more at https://sbgrid.org/news/sbgrid_cryoem_cloud_tournament. 

Our software webinar series will resume in October with Beata Turoňová, Group Leader at the Max Planck Institute of Biophysics, introducing cryoCAT, a library providing contextual analysis tools for cryo electron tomography and subtomogram averaging. Until then, you can catch up on webinars you missed from our last series on the SBGrid YouTube channel: https://www.youtube.com/user/SBGridTV

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

October 13: Beata Turoňová - cryoCAT

November 10: David Herreros - Scipion for flexibility using Hax

December 8: Yousef Metwally - TomoTwin-cryoet

January 12: Marten Chaillet - miss-alignment

February 9: Beata Turoňová - GAPSTOP(TM)

We're still finalizing speakers for the remainder of the series.

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 22 titles - AlphaFold3, AlphaPulldown, AmberTools, CCP4, Chromap, COOT, cryoDRGN, DIALS, Foldtree, ICM Browser, NMRFx-Anaylst, OpenFold3, Open Force Field Toolkit, OpenMM, pyCoAn, pytom-match-pick, RDKit, Scipion, Schrödinger, Warp, and XDS  -  along with 1 new applications: OCTOPI

See Software Changes below for complete details.

Four new members joined in the month of August: Scott Boyd from Stanford University, Stephen Ragsdale from University of Michigan Medical School, and Yoon Seok Kim and Angela Steinauer from École Polytechnique Fédérale de Lausanne.  Welcome to our newest members!

macOS 27 expected this fall

Apple is expected to release macOS 27 in the fall, and as with many new operating system releases, we recommend that users delay updating until the bugs are worked out. In the event that you buy a new machine or update for other reasons, please be sure to contact us at bugs@sbgrid.org to report any problems you encounter.

XDS licensing change 

XDS is now licensed through DECTRIS and will remain freely available for nonprofit users with the added bonus that time-bound version limitations no longer apply. The first release from DECTRIS is out (see software changes below for details). Industry members with an existing license will need to re-license XDS through DECTRIS to receive updated versions in your SBGrid collection. Please contact us at licensing@sbgrid.org with any questions.

Instruct-ERIC Webinar Series: Structure Meets Function 49 

September 15, 2026 | Virtual

Join to hear an overview of services available through 2 facilities that recently joined Instruct-ERIC: the European XFEL and Forschungszentrum Jülich.

Register here

Instruct-ERIC Industry Webinar - Mass Photometry to support Structural Biology Research

October 13, 2026 | Virtual

Join to learn about how to access Mass Photometry technologies through Instruct-ERIC and hear from scientists who have used Mass Photometry in their research.

Presented in collaboration with Refeyn

Register here

Instruct.SI CryoEM Workshop 2026, Single Particle Analysis

November 10-12, 2026 |  National Institute of Chemistry, Ljubljana, Slovenia

An in-person cryo-EM workshop designed to provide researchers with meaningful hands-on experience covering the entire cryo-EM workflow, from EM grid preparation to 3D reconstruction.

Application deadline: October 2, 2026

Register here.

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. 

- Lipscomb University student Vina Nguyen chose to highlight a publication in Nature Structural and Molecular Biology from the laboratory of Nikola Pavletich at Memorial Sloan Kettering Cancer Center in which researchers describe the structure of ATR-ATRIP complex bound to its two activators, revealing the mechanism behind one of the cell’s key DNA-damage checkpoints. [Learn more.]

- Meharry Medical College student Mudia Ikoba highlights a publication in Cancer Cell with contributions from Priyamvada Acharya and colleagues from Duke University School of Medicine where the authors explore the utility of antibodies produced by tumor-infiltrating plasma cells to guide cancer immunotherapy strategies. [Learn more.]

- Fisk University student Cariuna Ellison's highlight features a PNAS publication from  Kate Ferguson's laboratory at Yale University School of Medicine that appeared in PNAS. Ferguson's group identifies the activation mechanisms of an important protein receptor, EGFR, linked to cancer. [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 5 new citations since our last reporting, from these SBGrid members and contributing developers:

Peter Dahlberg from Stanford University in ACS Nano: Cryo-Electron Tomography Reveals Nanoscale Thick Filament Disorganization in MYH7 P710R Hypertrophic Cardiomyopathy Cardiomyocytes.

https://pubs.acs.org/ancac3/article/doi/10.1021/acsnano.6c03369/5272743

Eric Fischer from Dana-Farber Cancer Institute in Nature: DCAF11-dependent molecular glue degrader activated by glutathionylation.

https://www.nature.com/articles/s41586-026-10873-1

Andrew Kruse from Harvard Medical School in PNAS: Activation of the angiotensin II type I receptor by a nonpeptide agonist.

https://www.pnas.org/doi/abs/10.1073/pnas.2602538123

Bo Liang from Emory University School of Medicine in Microorganisms: Unreacted RSV Polymerase Structures Expand the Post-Translocation Landscape of the Nucleotide Addition Cycle.

https://www.mdpi.com/2076-2607/14/8/1801

Guy Schoehn from IBS Grenoble in Journal of Molecular Biology: High-resolution Structure of the Vaccinia Virus Phospholipase D-fold Endonuclease K4.

https://www.sciencedirect.com/science/article/pii/S0022283626003347

One new title was added to the SBGrid collection in August:

OCTOPI 1.6.0 is a deep-learning framework for automated 3D particle picking in cryo-electron tomography, with tools for training and running 3D U-Net models and automatically exploring model configurations. It supports local and remote tomography data.

https://github.com/Biohub/octopi

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

AlphaFold3 3.0.4 adds support for running on CPU-only systems. It also improves inference speed and memory use, restores unified-memory support on Blackwell GPUs, adds Google Cloud Storage paths and chain IDs to confidence summaries, and includes smaller validation and documentation fixes.
https://github.com/google-deepmind/alphafold3/releases/tag/v3.0.4

AlphaPulldown 2.6.1 improves AlphaFold3 metadata handling, preserving feature provenance across native AlphaFold3, AlphaPulldown-generated, AlphaFold2, and mixed inputs, and adds more complete ModelCIF metadata for the software, databases, parameters, and inputs actually used. It also introduces --storage_mode presets to reduce prediction-output size, fixes homooligomer naming and other compatibility issues.

https://github.com/KosinskiLab/AlphaPulldown/releases/tag/2.6.1

AmberTools 26 adds new system-building tools like the ProPrep workflow manager and a packmol-memgen GUI, and speeds LEaP/Antechamber handling of large systems and new formats. It also updates cpptraj (including a new build tool for prmtops), refines implicit-solvent models with dSASA, GBION, and a tensor-based GPU PB solver, and introduces new/updated force fields for lignin, RNA, and pGM electrostatics.

https://ambermd.org/AmberTools.php

CCP4 9.0.016 refreshes the ecosystem with newer backbone tools and GUIs, including Servalcat 0.4.142 with refmacat fixes, updated Coot-1, Moorhen 0.22.4, and new CCP4Cloud 1.8.014 and CCP4i2 2.6.3 builds across all major platforms.
https://www.ccp4.ac.uk/ccp4-9-0-updates/

CCP4 9.0.017 is a small maintenance release focused on stability, bug fixes, and minor improvements across the core suite and graphical interfaces. 

https://www.ccp4.ac.uk/ccp4-9-0-updates/

Chromap 0.3.3 - r521 fixes a bug in selecting the best mapping pair, improving paired-end alignment accuracy in edge cases while keeping the ultrafast chromatin-profile mapping workflow unchanged.

https://github.com/haowenz/chromap

COOT 1.3.3 adds an AI button for LLM-based interaction with Coot, enhances the Rotate/Translate Zone tool with direct click-drag moves and centered ctrl–shift–drag rotations, and introduces a new command terminal with completion and natural-language commands. It also supports PDBQT read/write for docking workflows, multi-pick water deletion, and KVFinder-style cavity detection with subpocket segmentation. 

https://github.com/pemsley/coot/releases/tag/Release-1.3.3

cryoDRGN 4.3.1 expands the interactive dashboard with integrated 2D slice and 3D volume viewing, improved trajectory creation, and custom color covariates for analysis plots. It also adds a utility for converting WarpTools/RELION 5 subtomogram data for use with cryoDRGN, broadens compatibility through Python 3.14, and fixes several dependency-related issues.
https://github.com/ml-struct-bio/cryodrgn/releases/tag/4.3.1

DIALS 3.30.0 expands serial crystallography support with a new SSX refinement workflow, improved scaling defaults, ΔCC½ filtering, and live processing of datasets while images are still being collected. It also adds XDS_ASCII export, wavelength/time-of-flight range controls, improved small-molecule handling in xia2, and fixes affecting multiprocessing, beam-position searches, image display, reports, and clustering output.
https://github.com/dials/dials/releases/tag/v3.30.0

Foldtree 1.1.1 contains minor technical changes and no longer creates or uses the ~/.foldtree directory.

https://github.com/DessimozLab/fold_tree/releases/tag/v1.1.1

ICM Browser 3.9.5 introduces Ligand AIDE for neural-network–driven de novo ligand generation, upgrades Gigasearch to v2.0 for ultra-fast substructure and similarity searching of vast chemical spaces, and extends the 3D interactive ligand editor with a comprehensive peptide modeling workflow. The Mac version is ARM-based only.

https://www.molsoft.com/icm_browser.html  

NMRFx-Anaylst 12.0.7 is out. No changelog is available.
https://github.com/nanalysis/nmrfx/releases/tag/v12.0.7

OpenFold3 0.4.5 improves cyclic-peptide prediction, adds pocket constraints for guiding ligand placement, and improves ligand stereochemistry agreement with the Chemical Component Dictionary.

https://github.com/aqlaboratory/openfold-3/releases/tag/0.4.5

Open Force Field Toolkit 0.19.0 fixes force-field serialization for virtual-site parameters with unset values, allowing affected VirtualSite definitions to round-trip correctly through ForceField.to_string() and to_file().

https://github.com/openforcefield/openff-toolkit/releases/tag/0.19.0

OpenMM 8.6.0 adds multi-state sampling with new replica-exchange and expanded-ensemble samplers, supporting workflows such as accelerated sampling and free-energy calculations.

https://github.com/openmm/openmm/releases/tag/8.6.0

pyCoAn 0.3-b675c7f includes minor bug fixes and preparations for the upcoming GoldX release.
https://github.com/pyCoAn/distro/releases/tag/03-b675c7f

pytom-match-pick 0.14.0 improves WarpTools/AreTomo compatibility, including support for sample-leveling angles and corrected CTF, wedge-orientation, and defocus-handling behavior. It also reworks whitening-filter estimation and fixes several issues affecting tilt-weighted wedges and phase-randomized noise correction.

https://github.com/SBC-Utrecht/pytom-match-pick/releases/tag/0.14.0

RDKit 2026.03.5 improves handling of molecular names and data groups, and validates coordinate constraints before 3D embedding. It also fixes several issues relating to stereochemistry, aromaticity, distance-geometry, fingerprint, molecule-fragmentation, and file-parsing.
https://github.com/rdkit/rdkit/releases/tag/Release_2026_03_5

Scipion 3.11.6 includes a CryoSPARC plugin update, which improves cryoSPARC v5 connection checks for multi-user installations, adds support for custom cryosparcm commands through CRYOSPARCM_CMD and fixes import of CryoSPARC v5 particle .cs files when particle stacks are stored as .mrc files. Also new in the Scipion SBGrid installation: the Scipion-em-miffi plugin. This plugin provides a wrapper for miffi software tools for automatic micrograph assessment.

CryoSPARC plugin: https://github.com/scipion-em/scipion-em-cryosparc2/pull/205 

miffi plugin: https://github.com/scipion-em/scipion-em-miffi/tree/v1.1.0 

Schrödinger 2026-3 adds Rapid Binding Site Similarity for comparing protein binding sites against the PDB or custom libraries, faster Desmond simulations through adjustable hydrogen mass repartitioning, and new FEP+ workflows including faster ABFEP scanning and large-scale Protein FEP residue scanning. This release also expands macrocycle modeling and docking, adds improved GPCR support in Maestro and protein preparation, and includes a broad range of workflow and interface improvements across structure analysis, docking, molecular dynamics, and lead optimization.
https://www.schrodinger.com/life-science/download/release-notes/

Warp 2.0.0dev40 adds cluster-based processing through scheduler support and a more robust filesystem queue for distributed workers, with improved fault tolerance, logging, and job recovery. It also adds non-premultiplied particle export and preserves custom particle metadata, while fixing several issues relating to RELION export, Noise2Map, CTF, symmetry-expansion, and multi-GPU processing.

https://github.com/warpem/warp/blob/main/CHANGES.md#v200dev40

XDS 20260616 is the first release since DECTRIS took over development and distribution. This release includes improvements to integration (background estimation and output header expansion) and removal of the time limitation that expired the executables xds, xds_par, xscale, and xdsconv.

https://dectris.com/en/detectors/XDS/

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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