SBGrid Newsletter: February 2026

Dear Consortium Members and Affiliates,

Our February update includes news on a change to SBGrid's default citation, a reminder about upcoming and recent webinars, a software push with 13 updates and three new titles, two new members to welcome, new documentation on using SBGrid on HPC resources, position postings from the laboratory of Antonina Roll-Mecak, and two publication highlights from our student desk. 

We've updated SBGrid's primary citation to our 2024 Acta Crystallographica  paper, which provides a more comprehensive description of the SBGrid environment, its architecture, and current capabilities. We would be grateful if you could use this reference in future manuscripts, preprints, and related work where appropriate.

Join our software webinar on March 10th to hear from Josh Mitchell from the Open Molecular Software Foundation on Open Force Field. This presentation is a follow up to last month's webinar when we heard from Alyssa Travitz on Open Free Energy, the recording for which is now 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

March 10:  Josh Mitchell  - Open Force Field

April 14: Jose Luis Vilas - Image processing made it simple with scipionTomo

May 12: Jarrett Johnson - Upcoming improvements to visualization and CryoEM support in PyMOL

June 9: Mart Last -  Ais and Pom

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 Ais, AlphaFold3, Boltzgen, Bowtie2, CellProfiler, ChimeraX, CryoMaskR, CryoSPARC-tools, Foldseek, IsoNet2, Protenix, RDKit, and upside2-md, along with three new titles: easymode, mBER-open, and vossvolvox.

See Software Changes below for complete details.

Two new members joined during the past month: Krishna Reddy from University of South Florida and Dylan Hale from University of Pittsburgh.

Welcome to our newest members!

SBGrid on HPC: We've published some initial documentation on using individual or group SBGrid installations on HPC resources where creating a `/programs/` link is problematic. Please contact us at accounts@sbgrid.org if you encounter problems or identify areas for improvement. We welcome your feedback  Learn more about Using SBGrid Programs on HPC Clusters with Apptainer: https://docs.sbgrid.org/usage/apptainer/ 

Phenix 2 / Coot 1 integration update: The Phenix/Coot GUI integration is not currently working; the Phenix developers are targeting a fix for their next official release.

Postdoc and Postbac | Antonina Roll-Mecak | NIH

A postdoctoral fellowship and postbac position are available in the Cell Biology and Biophysics Unit headed by Dr. Antonina Roll-Mecak to work on mechanisms of microtubule cytoskeleton regulation in iPSC derived human neurons with a focus on the role of the tubulin code. The project combines in vitro reconstitution, superresolution fluorescence microscopy and cryogenic electron tomography to capture the structure and dynamic behavior of the cytoskeleton and its alteration in neurodegeneration. The successful candidate will work collaboratively with the Advanced Imaging & Microscopy center at the NIH (https://www.nibib.nih.gov/labs-at-nibib/advanced-imaging-and-microscopy-aim-resource) and will benefit from a collaborative co-mentored experience. We are looking for Ph.D. graduates with a strong record of accomplishments and expertise in cell biology, biochemistry, single molecule biophysics, light microscopy, or cryo-EM.  The NIH has an outstanding neuroscience and structural biology community, and the lab has regular access to state-of-the-art resources such as TIRF, iSIM and lattice sheet microscopes, Chameleon, Krios with K3 camera as well as Aquilos 2 cryo-FIB. Please send your CV, a one-page research experience summary and contact information of three references to Antonina@nih.gov  Please write “Tubulin code” in the subject header. Visit the lab website for more information:

https://www.ninds.nih.gov/about-ninds/who-we-are/staff-directory/antonina-roll-mecak

Nearly 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. This month we are pleased to have our first contribution from Mudia Ikoba from Meharry Medical College.

- Fisk University student Cariuna Ellison's highlight features a publication from Fengbin (Jerry) Wang of University of Alabama at Birmingham that appeared in Emerging Topics in Life Sciences and describes their use of Cryo-EM to identify the biological "power cords" bacteria use to export electricity. [Learn more.]

- Meharry Medical College student Mudia Ikoba chose to highlight a publication in Nature Communications from the laboratory of Edward Twomey of Johns Hopkins University School of Medicine in which the authors characterize structural features of the AMPA-subtype glutamate receptor GluA4 subunit using cryoEM to clarify functionality within the protein. [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:

James Berger from Johns Hopkins University School of Medicine in Nature Communications: Supercoiled DNA recognition and cleavage control in topoisomerase VI.

https://www.nature.com/articles/s41467-026-69491-0

Eric Fischer from Dana-Farber Cancer Institute in Nature Chemical Biology

High-throughput ligand diversification to discover chemical inducers of proximity.

https://www.nature.com/articles/s41589-025-02137-2

Oriana Fisher from Wesleyan University and Titus Boggon from Yale University in Nature Communications: Dual recruitment of two CCM2 molecules to KRIT1 suppresses KLF4 expression.

https://www.nature.com/articles/s41467-026-69595-7

Christopher Garcia from Stanford University School of Medicine in Science:  Structural ontogeny of protein-protein interactions.

https://www.science.org/doi/full/10.1126/science.adx6931

Alireza Ghanbarpour from Washington University School of Medicine, St. Louis in Nature: Bacterial immune activation via supramolecular assembly with phage triggers. https://www.nature.com/articles/s41586-025-10060-8

Anthony Kossiakoff from The University of Chicago in PNAS: Conformational ensembles of the magnesium channel CorA reveal structural basis for channel gating. 

https://www.pnas.org/doi/abs/10.1073/pnas.2512532123

Philip Kranzusch from Dana-Farber Cancer Institute in Nature: Nucleotide signals coordinate activation and inhibition of bacterial immunity.

https://www.nature.com/articles/s41586-026-10135-

Woonghee Lee from University of Colorado, Denver in Journal of Biological Chemistry: Modernizing Biomolecular NMR: the POKY Suite.

https://www.sciencedirect.com/science/article/pii/S002192582600116X

John Pascal from University of Montreal in Nature Communications: PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation.

https://www.nature.com/articles/s41467-026-69375-3

Edward Twomey from Johns Hopkins University School of Medicine and Dylan Hale (now at University of Pittsburgh) in Nature Communications: Structural basis for activation and conformational plasticity of the GluA4 AMPA receptor.

https://www.nature.com/articles/s41467-026-68953-9

Elizabeth Wright from University of Wisconsin, Madison in Nature Protocols: Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET.

https://www.nature.com/articles/s41596-025-01284-z

easymode 57ba482 is a collection of general pre-trained networks trained on a large, curated body of cryoET datasets for feature detection in cellular cryoET. The models are hosted via Hugging Face and automatically distributed for inference, which means you don't need to download model weights.

https://mgflast.github.io/easymode/ 

mBER-open 20260205 is a protein design framework for antibody binder design that leverages structure templates and sequence conditioning in backpropagation-based design through AlphaFold-Multimer. This tool enables format-specific binder design with a modular architecture built around three key modules: Template (prepares target structures and identifies hotspots), Trajectory (designs binder sequences using protein folding models and optimization), and Evaluation (assesses designed binders using various metrics). It includes a command-line interface for VHH (nanobody) binder design and was experimentally validated with million-scale screening.

https://github.com/manifoldbio/mber-open/tree/main

vossvolvox 1.0 is a suite of command-line tools for the reproducible grid-based analysis of molecular structures, including the computation of volumes, channels, cavities, and tunnel geometry. It supports multiple input formats such as PDB, mmCIF, PDBML, and XYZR, providing a unified interface for geometric molecular analysis. 

https://github.com/vosslab/vossvolvox/

Ais 1.0.47-e941fb8 is now available.

https://github.com/bionanopatterning/Ais/commits/master/ 

AlphaFold3 was redeployed as a standalone title due to licensing differences between AlphaFold2 and AlphaFold3. In addition to this correction, commit 22b9ab8 is now available for AlphaFold3. This unofficial release has no changelog, but includes new functionality that users are eager to try and is now available via version override.

https://github.com/google-deepmind/alphafold3/commits/main/ 

Boltzgen 0.3.0 includes significant enhancements, such as support for symmetric inverse folding and a new protein-redesign protocol. This version also introduces covalent bond constraints from file and SMILES specification, along with improvements in metrics computation and scoring normalization for small molecules. Additionally, various bug fixes enhance stability and functionality, making it a recommended update for users.

https://github.com/HannesStark/boltzgen/releases/tag/v0.3.0

Bowtie2 2.5.5 is focused on enhanced stability and performance for high-throughput sequence alignment. This version introduces critical fixes for memory scaling when processing large BAM files and improves the robustness of the bowtie2-build indexing process. It also ensures that output flushing is maintained during partial writes and includes a revamped FASTQ parser that is more resilient to empty lines and compressed input streams.

https://bowtie-bio.sourceforge.net/bowtie2/

CellProfiler 4.2.8 is a maintenance and stability update that resolves label assignment errors for neighboring objects of different types (bug #4929), upgrades to CellProfiler-core 4.2.8 for improved framework compatibility, formally introduces verified builds for macOS 13+ (Intel and ARM) and Windows 10/11, and updates package pins and wheels to streamline installation via pip on modern Python environments.

https://github.com/CellProfiler/CellProfiler/releases/tag/v4.2.8

ChimeraX 20260215 is a daily build with bug fixes related to the OpenFold integration with ChimeraX version 1.11.

https://github.com/RBVI/ChimeraX/commits/develop/ 

CryoMaskR is now available for Linux (the MacOS version was released previously).

https://github.com/mcalbyrne/cryomaskr/releases/tag/v1.0.1-linux

CryoSPARC-tools 5.0.1 is a significant update for compatibility with the latest CryoSPARC version. It adds support for Python 3.14, a safer login, new search (find_*) methods, and improved metadata and typing, while simplifying networking requirements. It also unifies functionality under CryoSPARC.api, replaces dictionary-style returns with cleaner object models, and tightens rules around modifying external jobs. Several older functions and arguments were deprecated or removed.

https://github.com/cryoem-uoft/cryosparc-tools/releases 

Foldseek 10-941cd33 introduces GPU support for both monomer and multimer searches, significantly accelerating search times by up to 37x on multi-GPU setups. This release also enhances structural profile searches, integrates ProstT5 with improved handling of large sequences, and introduces a new virus-specific database: BFVD. Optimizations for multimer workflows and experimental clustering features are also included, alongside bug fixes and improved compatibility with MMseqs2 modules.

https://github.com/steineggerlab/foldseek/releases/tag/10-941cd33

IsoNet2 was updated in SBGrid under a new versions for CLI (2.0.0-beta) and GUI (2.0.0-beta-gui) to resolve some issues.

https://github.com/IsoNet-cryoET/IsoNet2/tree/IsoNet-2.0.0-beta

Protenix 0.7.3 Fixes the bug in the code where ref_space_uid was mistakenly written as ref_mask in the cache computation.

https://github.com/bytedance/Protenix/releases/tag/v0.7.3 

RDKit 2025.09.5 includes significant performance improvements, such as buffered reading for SDMolSupplier and enhanced handling of molzip fragment positioning. This release also fixes numerous bugs, including issues with hydrogen bond acceptor counts and implicit hydrogen labeling, ensuring more reliable molecular data processing. Deprecated code has been noted for future removal, streamlining the software's functionality.

https://github.com/rdkit/rdkit/releases/tag/Release_2025_09_5

upside2-md 1.0.0_9476137 is the second-generation version of a coarse-grained molecular dynamics (MD) engine designed specifically for protein physics. Developed by the Sosnick Lab at the University of Chicago, it allows for rapid protein folding simulations using a simplified model of three backbone atoms per residue and rapid side-chain packing.

https://sosnick.uchicago.edu/research/upside.html 

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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