SBGrid Newsletter: July 2026

Dear Consortium Members and Affiliates,

As we step into August and what are hopefully some quieter summer days before the academic season ramps up again, our update includes a recording of our July webinar, a call for suggestions for our next season of webinars, a software push with updates to 20 applications and four new titles, four new members to welcome, a listing of upcoming events from our partners at Instruct-ERIC, and publication highlights from two of our student contributors featuring work from the laboratories of Youxing Jiang and Mihnea Bostina.

We finished our 2025-2026 Software Webinar season in July with a presentation from Mart Last on Ais, Pom, and easymode. In case you missed it, you can find the recorded version on the SBGridTV YouTube channel: https://www.youtube.com/watch?v=YpZ2G2TpLLA

Our lineup for the the 2026-2027 season is coming soon. If there is a software title you'd like to know more about, please contact us at accounts@sbgrid.org with your suggestions.

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 20 titles  ---  BCFtools, Blast+, Chimera, CcpNmr Analysis, Fiji, GROMACS, Icecream, IMOD, LigPlot+, MODELLER, NMRPipe, OpenEye, OpenFold3, RDKit, SAMtools, Schrödinger, Scipion, TEMPy-ReFF, tomoDRGN, and Warp  ---  along with four new applications: copick, DisVis, Hax, and Leopard-EM.

See Software Changes below for complete details.

Four new members joined in the month of July: Hector Aguilar-Carreno from University of California, Los Angeles, Arthur Neuberger from Ludwig Maximilians Universität München, Lisa Olshansky from University of Illinois at Urbana-Champaign, and Taha Shahid from the University of Birmingham.

Welcome to our newest members!

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. 

- Fisk University student Cariuna Ellison's highlight features a publication from Youxing Jiang at UT Southwestern Medical Center that appeared in Nature Communications and describes their investigation of a small molecule, NC1, that activates a cancer ion channel, leading to overload and cancer cell death. [Learn more.]

- Welcome to Vina Nguyen of Lipscomb University, a new contributor to our student desk! Vina chose to highlight a publication from the laboratory of Mihnea Bostina at University of Otago that appeared in Journal of Molecular Biology in which the authors describe how the newly found structure of Bas18 provides a reference tool to bacterial viruses, with potential uses in therapeutics, vaccines, and food safety. [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:

Eric Fischer from Dana-Farber Cancer Institute in Science: Degron-independent recruitment of KAT2A expands the target space of CRBN molecular glues.
https://www.science.org/doi/abs/10.1126/science.aef5391

Chi-Min Ho from Columbia University in Cell: Structural basis for host membrane binding and remodeling by invading malaria parasites.

https://www.cell.com/cell/fulltext/S0092-8674(26)00699-9

Aravindan Ilangovan from Queen Mary University in Nucleic Acids Research:
Bacillus subtilis DnaB forms multiple protein–protein interactions essential for DNA replication initiation.
https://academic.oup.com/nar/article/54/12/gkag630/8723642

Andrés Palencia from Université Grenoble Alpes in Journal of the American Chemical Society: Alternative Splicing of a Structured Partner Alters the Folding-Upon-Binding Trajectory of an Intrinsically Disordered Protein.
https://pubs.acs.org/jacsat/article-abstract/148/27/28401/5169775/Alternative-Splicing-of-a-Structured-Partner

Pedro Pereira from Universidade do Porto in Protein Science:  A cryptic aromatic binding pocket in the highly thermostable GpgS from Mycobacterium hassiacum hints at MGLP pathway crosstalk.
https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.70713

Karin Reinisch from Yale University School of Medicine in Molecular Cell: Cryo-EM structure of soluble VPS13C suggests its regulation by a conformational switch and by calmodulin.
https://www.cell.com/molecular-cell/fulltext/S1097-2765(26)00417-X

Frank Sicheri from University of Toronto in Nature Communications Chemistry:
Structure and mechanism of inhibition of lysine demethylase 2A (KDM2A) by compound 183c.
https://www.nature.com/articles/s42004-026-02100-9

Four new titles were added to the SBGrid collection this month:

copick  is a cross-platform, storage-agnostic, and server-less dataset API for cryoET datasets. Access to the data is provided through an object-oriented API that abstracts away the underlying storage using the fsspec-family of libraries. Available at version 1.26.1 

https://copick.github.io

DisVis is a Python package and command line tool to visualize and quantify the accessible interaction space of distance restrained binary biomolecular complexes. It performs a full and systematic six-dimensional search of the three translational and rotational degrees of freedom to determine the number of complexes consistent with the restraints. It also outputs the percentage of restraints being violated and a density that represents the center-of-mass position of the scanning chain corresponding to the highest number of consistent restraints at every position in space. Available at version 2.3.0.
https://github.com/haddocking/disvis

Hax is a suite for heterogeneity analysis of CryoEM data that includes several tools to study conformational heterogeneity: heterogeneity analysis programs, consensus of conformational landscapes, annotation of conformational landscapes, and reconstruction of motion corrected. Available versions: volumes.1.0.3_cu12, 1.0.3_cu13. 
https://github.com/DavidHerreros/hax-em/tree/main

Leopard-EM  (Location & oriEntatiOn of PARticles found using two-Dimensional tEmplate Matching) is a python package for running two-dimensional template matching (2DTM) on cryo-EM images. Available at version 1.2. 
https://lucaslab-berkeley.github.io/Leopard-EM/

New releases or versions added for these existing titles in the SBGrid collection:

BCFtools 1.24 introduces a new +trio-dnm3 model as the default for de novo mutation calling, adds --no-realign[=NUM] to norm (deprecating --do-not-normalize), fixes MAC/MAF calculations at multiallelic sites, adds merge -m exact for allele-identical merging, corrects INFO/END recalculation of symbolic alleles, and fixes a bug in splitting Type=String FORMAT fields. Ambiguous IUPAC bases are now converted according to VCF spec.
https://github.com/samtools/bcftools/releases

Blast+ 2.17.0 adds support in makeblastdb for building databases directly from FASTA files compressed with gzip, bzip2, or zstd, introduces a CSV output format with headers to streamline downstream parsing, and speeds up protein searches when using the -task blastp-fast option. It also resolves a stability issue that could cause jobs to hang, and incorporates all fixes made in version 2.16.0 and earlier.
https://blast.ncbi.nlm.nih.gov/doc/blast-news/2025-BLAST-News.html#download-blast-2-17-0-now

Chimera 1.20 fixes problems on Mac OS Tahoe including, finding OpenGL library and main graphics window mis-positioning.
https://www.cgl.ucsf.edu/chimera/docs/relnotes/1.20.html

CcpNmr Analysis 3.4.0 is the newest release. No changelog is available.
https://ccpn.ac.uk/software/downloads/

Fiji 2.16.0 aligns the Fiji distribution with ImageJ2 2.16.0, introducing support for newer Java runtimes (up to Java 21) and updating bundled components such as Bio-Formats (now based on the 7.3.1 line) to improve compatibility with recent microscopy file formats and analysis plugins. This release is primarily an infrastructure and dependency refresh and folds in fixes from Fiji 2.14.0 and earlier.
https://fiji.sc/

GROMACS 2026.3 addresses changes that have taken place since the previous 2026.2 version, to fix known issues and includes fixes where mdrun could behave incorrectly, fixes for gmx tools, updated documentation, and warnings in gmx angle. It also incorporates all fixes made in version 2025.4 and earlier.

https://manual.gromacs.org/documentation/2026.3/release-notes/2026/2026.3.html

Icecream 0.4 adds support for multi-GPU training, which internally uses torch's distributed dataparallel to distribute the training across multiple GPUs. Also new are integration tests for training commands and an option for using multiple gpus accessible with a devices argument in your cli, for example: --device 0,1
https://github.com/swing-research/icecream/blob/main/CHANGELOG.md

IMOD 5.1.12 includes multiple bug fixes. The mac version targets Mac OS 12 - 26 running on an arm64 (M1, M2, etc) processor.
https://bio3d.colorado.edu/imod/#Release%20Notes

LigPlot+ 2.3.2 is a maintenance release focusing on improved robustness when generating ligand–protein interaction diagrams from PDB structures and compatibility updates to keep pace with current docking and visualization workflows. It consolidates prior bug fixes and minor performance improvements from the 2.2.x series and earlier.
https://www.ebi.ac.uk/thornton-srv/software/LigPlus/

MODELLER 10.8 includes model-assessment scores in mmCIF output from AutoModel and LoopModel using standard ModelCIF tables.
https://salilab.org/modeller/release.html

NMRPipe 20260520 is now available. No changelog was found

OpenEye 2025.2.3 delivers minor bug fixes and updated dependencies to 2025.2.1, which introduced more flexible molecular and grid-based searches, the new Saiph toolkit for easier file conversion and data preparation, and stronger mmCIF support for working with macromolecular structures.
https://docs.eyesopen.com/applications/notes/releasenotes/highlights.html

OpenFold3 0.4.4 fixes template handling during inference, replaces the default inference kernel as part of moving away from DeepSpeed kernels, and ensures that max_seq_count correctly limits parsed multiple-sequence alignments.
https://github.com/aqlaboratory/openfold-3/releases/tag/0.4.4

RDKit 2026.03.4 improves molecular coordinate generation with spiro-ring flipping and refined ETKDG conformer generation, doubles the performance of synthon substructure searches, and makes long substructure searches interruptible. It also adds configurable stereochemistry labels and multi-conformer Gaussian shape support, alongside fixes for molecular drawing, InChI and ChemDraw stereochemistry handling, R-group decomposition, and highlighted structure rendering.
https://github.com/rdkit/rdkit/releases/tag/Release_2026_03_4

SAMtools 1.24 introduces functional updates including a more robust default seed behavior for samtools view --subsample based on file headers, a new option to move UMIs to tags in markdup, mate information backfilling in fixmate, and notable speed and bug fixes for samtools stats. Additional improvements include indirect function call type checking, biobambam2 checksum compatibility, and minor command-line option cleanups to match other subcommands.
https://github.com/samtools/samtools/releases

Schrödinger 2026-2 improves structure-based drug-discovery workflows with easier crystal-contact diagnostics and side-chain reconstruction during protein preparation, automatic SiteMap rescoring for mixed-solvent MD, command-line MacroDock support, and faster FEP+ cycle-closure calculations. Maestro also gains improved search and structure-selection tools, while biologics workflows add faster protein-descriptor calculations, non-standard amino-acid database creation, and greater control over antibody modelling templates.
https://www.schrodinger.com/life-science/download/release-notes/

Scipion 3.11.6 includes many new plugins: scipion-em-imod v3.9.1, which brings support for IMOD 5.1.3, scipion-em-emantomo v3.4.2, scipion-em-reliontomo v4.0.4, scipion-em-tomo v3.12.0, scipion-em-sphire v3.2.6, scipion-em-topaz v3.1.2, scipion-em-aretomov4.0.0, scipion-em-fidder v3.2.2, scipion-em-hax v1.0.1 (flexibility analysis), and scipion-em-cryosparc2 v5.0.0, which brings compatibility with CryoSPARC 5.0.x. Please keep in mind that CryoSPARC is not available in SBGrid. You will need to link your existing CryoSPARC install to Scipion SBGrid following these instructions.

TEMPy-ReFF 1.2 brings several fixes and improvements including a new function to join NAG to ASN if a bond is missing, handling of N-linked glycosylation for some common sugars under AMBER, as well as better residue fixing logic, handling of disulfide bonds, and breaking chains into contigs.
https://gitlab.com/topf-lab/tempy-reff/-/commits/v1.2.0?ref_type=tags

tomoDRGN 1.0.4 improves multi-GPU training and volume generation, including fixes for model encoding and decoding across multiple GPUs. It also updates handling of CTF-premultiplied and dose-weighted particle images and reverts the voxel back-projection command to its previous implementation.
https://github.com/bpowell122/tomodrgn/releases/tag/v1.0.4

Warp 20260714 includes an --extract_raw flag for ts_export_particles to store particle series without dose weighting and CTF premultiplication, along with other fixes.

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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