SBGrid Newsletter: January 2026 |
Dear Consortium Members and Affiliates, For our inaugural 2026 newsletter, we are sharing a profile on SBGrid member Jean-Philippe Julien, news about upcoming and recent software webinars, a software push that includes 15 updates and 10 new titles, a welcome to nine new members, a reminder that users can request personal installation manager credentials, and one member publication highlight.
Our January member tale features Jean-Philippe Julien from The Hospital for Sick Children in Toronto, who interrogates antibodies in the science of global heath, following their stories to guide interventions against infectious diseases like malaria. Julien credits the ethos of his undergraduate college for nurturing his early humanitarian interests and fostering a culture of peace through understanding, the kind of mission-driven international collaboration that he now cultivates in his laboratory. [Read More]
Join our software webinar on February 10th to hear from Alyssa Travitz of the Open Molecular Software Foundation on Open Free Energy: An Open Source Ecosystem for Calculating Free Energies. If you missed Alice-Roza Eruera's January webinar on Building CryoET Training Workflows Using the SBGrid Ecosystem, we will have the video posted to the SBGrid YouTube channel soon. You can subscribe at https://www.youtube.com/user/SBGridTV to receive alerts when new videos are added.
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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February 10: Alyssa Travitz - Open Free Energy: An open source ecosystem for calculating free energies 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. |
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This month's software push includes updates to 15 titles -- anvi’o, BioXTAS RAW, ChemEx, CryomaskR, DeepRank-GNN-esm, DSSR, GROMACS, Icecream, IMP, PowerFit, PyEM, RDKit, SRAToolkit, Volume_Seg_Tool, and XDS -- along with ten new titles: Calc_level_chimerax, ConSurf, Foundry, ImmuneBuilder, IsoNet2, LASErMPNN, MagCalEM, Slabify, ThermoMPNN, and ThermoMPNN-D.
See Software Changes below for complete details.
Nine new members joined in the month of January: Javid Babak and James Chen from University of California, San Francisco, Daniel Castaño from Biofisika Institute, Joana Fort from University of Barcelona, Fangyu Liu from UT Southwestern Medical Center, Maria Oliva-Blanco from Margarita Salas Center for Biological Research, Esther Ortega from Centro Nacional de Biotecnologia, Martin Schmeing at McGil University, and Anne Marie Wehenkel along with the Image Analysis Hub, under the direction of Jean-Yves Tinevez, at Instiut Pasteur.
Welcome to our newest members! |
Personal Installation Credentials Users who currently only have access to the SBGrid software collection through a common site installation may also benefit from access to the collection on personally managed laptops or desktops in the laboratory or at home. This option: Keep in mind that large titles may take a long time to download, so be sure to plan ahead and make sure you have the required disk space.
Register for personal credentials here: https://sbgrid.org/registration/register/
Learn more on our wiki: https://docs.sbgrid.org/installation/installing_sbgrid/
Contact us with additional questions accounts@sbgrid.org |
Member Publication Highlights |
Over 100 new member publications appeared in journals this month. You can find a complete listing on our website. |
From our undergraduate student desk |
We're pleased to welcome Cariuna Ellison of Fisk University to our undergraduate desk, where we 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 JCI Insight publication from the laboratory of Chuck Sanders at Vanderbilt University in which the authors describe a small molecule that may change the trajectory of LQTS intervention research. [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. |
SBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications. Please use this SBGrid logo on the acknowledgements slide of your presentations.
We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software: |
Structural biology applications used in this project were compiled and configured by SBGrid [1]. [1] A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.
Link to article: https://elifesciences.org/articles/01456. |
Calc_level_chimerax 1.0.0 is a new ChimeraX plugin to predict and visualize isosurface levels for 3D density maps. This tool is based on a 3D-CNN initially developed to predict the isosurface levels of 3D density maps, as required by SIREn.
https://github.com/mariacarreira/calc_level_ChimeraX/releases/tag/v1.0.0
ConSurf 1.0.0 is a bioinformatics tool designed for estimating the evolutionary conservation of amino and nucleic acid positions in protein, DNA, and RNA molecules. It leverages phylogenetic relationships among homologous sequences to assess conservation, providing insights into structural and functional importance. ConSurf employs advanced computational methods, including empirical Bayesian and maximum likelihood approaches, to deliver accurate evolutionary rate estimations.
https://github.com/Rostlab/ConSurf
Foundry 0.1.7 is a unified framework for protein design that provides tooling and infrastructure for using and training models including RFdiffusion3 (all-atom generative design), RosettaFold3 (structure prediction), and ProteinMPNN/LigandMPNN (inverse folding). All models rely on AtomWorks, a unified framework for manipulating and processing biomolecular structures for both training and inference. This package enables end-to-end protein design workflows from structure generation through sequence design and validation.
https://github.com/RosettaCommons/foundry
ImmuneBuilder 0df4e2a is a deep-learning framework developed by the Oxford Protein Informatics Group for predicting the 3D structures of immune proteins, including antibodies (ABodyBuilder2), nanobodies (NanoBodyBuilder2), and T-cell receptors (TCRBuilder2).
https://github.com/oxpig/ImmuneBuilder
IsoNet2 is a deep-learning software package for simultaneous missing wedge correction, denoising, and CTF correction in cryo-electron tomography reconstructions using a deep neural network trained on information from the original tomogram(s). Compared to IsoNet1, IsoNet2 produces tomograms with higher resolution and less noise in roughly a tenth of the time. Versions with and without a GUI were added to SBGrid. https://github.com/IsoNet-cryoET/IsoNet2/tree/IsoNet-2.0.0-beta
LASErMPNN 0.4.0 is an all-atom ligand-conditioned protein sequence design and sidechain packing model that accounts for the presence of small molecules, including hydrogens. It utilizes a ligand-conditioned Message Passing Neural Network architecture to design sequences for specific binding sites and can perform both de novo design and sidechain repacking. This tool is trained on protonated structures to ensure accurate physical modeling of protein-ligand interactions.
https://github.com/polizzilab/LASErMPNN/tree/main
MagCalEM 1.3.2 provides a precise way to calibrate magnification in single-particle cryo-EM experiments. Using known atomic lattice spacings from simple reference samples like gold, it determines the true pixel size with better than 0.5% accuracy at both room temperature and cryogenic conditions, improving resolution, model accuracy, CTF estimation, and making it easier to combine datasets from different microscopes and detectors.
https://www.mrc-lmb.cam.ac.uk/crusso/magCalEM/index.html
Slabify 0.3.0 is a command-line tool designed for the automatic segmentation of lamella slabs in cryo-electron tomography (cryo-ET) volumes. It utilizes local variance analysis to identify significant density regions and offers multiple operational modes, including robust plane fitting and manual boundary definition. This tool is particularly useful for enhancing particle picking and optimizing template matching in cryo-ET data processing.
https://github.com/CellArchLab/slabify-et
ThermoMPNN v1.0.0 is a graph neural network (GNN) designed to predict changes in stability for protein point mutants using transfer learning. This tool provides insights into protein stability alterations due to mutations. It supports customizable output locations for inference, enhancing usability in various computational environments.
https://github.com/Kuhlman-Lab/ThermoMPNN
ThermoMPNN-D 20260107 is a Siamese neural network designed to predict stability changes from protein double point mutations. The tool extends ThermoMPNN and ProteinMPNN, offering three prediction modes: single mutant, additive double mutant (which sums individual contributions), and epistatic double mutant (which captures epistatic interactions between mutations). It provides fast inference through batched predictions and includes tools for systematic analysis of all possible single or double mutants in a protein structure, outputting mutation and ΔΔG values.
https://github.com/Kuhlman-Lab/ThermoMPNN-D |
anvi’o (“marie”) After about 4,200 changes that introduced over 36,000 new lines of code, this stable release of anvi'o represents significant advancements over v7, and introduces many new features for integrated studies of microbial metabolism, genomic inversions, phylogeography of proteins, performance improvements, and fixes for known bugs.
https://github.com/merenlab/anvio/releases/v8
BioXTAS RAW 2.4.1 includes significant improvements including a new workspace save format using .hdf5 files, which enhances compatibility and reduces file sizes. This release also addresses multiple bugs, including issues with multi-series analysis and compatibility with ATSAS 4.1.3, ensuring a more stable and efficient user experience.
https://sourceforge.net/p/bioxtasraw/news/2026/01/raw-241-released/
ChemEx v2025.10.0 includes a new 4-state Eyring model for chemical exchange kinetics analysis and enhanced state detection options for various experiments. This release also features significant documentation updates with a complete overhaul of the installation guide and new guides for two-spin system initial conditions and the 13CH3 13C CPMG experiment. It also addresses a bug related to initial conditions for two-spin systems and updates several dependencies to support Python 3.13.
https://github.com/gbouvignies/ChemEx/releases/tag/v2025.10.0
CryomaskR v1.0.1 includes a new license agreement popup requiring user registration upon first launch, enhancing compliance and user tracking. Significant improvements feature real-time selection overlays for better visual feedback, smoother lasso drawing, and larger selection circles for improved visibility, alongside atom clipping enhancements to exclude non-relevant atoms from selection. https://github.com/mcalbyrne/cryomaskr/releases/tag/v1.0.1
DeepRank-GNN-esm v0.3.0 now uses the model name instead of the model path in the get_embedding function, streamlining the process for users. This update enhances usability and improves the integration of model management within the software.
https://github.com/haddocking/deeprank-gnn-esm/releases/tag/v0.3.0
DSSR 2.7.2 is the latest update. No changelog is available. GROMACS 2025.4 fixes some known issues of the previous version 2025.3.
https://manual.gromacs.org/2025.4/release-notes/2025/2025.4.html
Icecream 0.3.1 includes multiple volumes training, more explicit parameters, and a bug fix related to missing wedge correction.
https://github.com/swing-research/icecream/releases
IMP 2.23.0 focuses on better file support, speed, and usability. IMP now more seamlessly handles modern structure formats (including BinaryCIF), with smarter readers and fixes. Several core scoring functions are significantly faster. There are also improvements for model handling, updated platform support (newer Linux), and a couple of important bug fixes that improve stability and reliability. https://integrativemodeling.org/2.23.0/doc/manual/changelog.html
PowerFit 4.0.3 introduces report coloring functionality to enhance the visualization of results when fitting atomic structures to cryo-electron microscopy density maps.
https://github.com/haddocking/powerfit/releases/tag/v4.0.3
PyEM 0.68 enhances compatibility and reliability for users relying on numpy functionalities. https://github.com/asarnow/pyem/releases/tag/v0.68
RDKit 2025.09.4 includes significant enhancements such as the addition of an API for extracting molecular fragments and performance improvements in bond determination functions. Users can now ignore hydrogen atoms in RMSD alignment functions and have support for custom atom and bond matcher functions for substructure searching. Numerous bug fixes and code cleanups further enhance stability and performance, making it a valuable update for users focused on cheminformatics and molecular modeling.
https://github.com/rdkit/rdkit/releases/tag/Release_2025_09_4
SRAToolkit 3.3.0 introduces support for reads longer than 65k in fasterq-dump and adds compatibility for the Salus and Geneus sequencing platforms. This update improves directory path and file type handling across multiple tools (including prefetch and vfs) and fixes a vdb-dump segmentation fault that occurred with empty platform columns. This release also standardizes Linux builds on AlmaLinux 8, updates read-filter-redact to set quality scores to 0 when masking reads, and officially deprecates Javadocs for the toolkit.
https://github.com/ncbi/sra-tools/blob/master/CHANGES.md
Volume_Seg_Tool v0.10.3 includes a simple requirement.txt and UI updates to ensure compatibility with the latest Gradio version. This release focuses on enhancing user experience and maintaining software functionality with recent dependencies.
https://github.com/fgdfgfthgr-fox/Volume_Seg_Tool/releases/tag/v0.10.3
XDS 20251103 includes a few changes to output formats, and eliminates the requirement for a dynamic library (libquadmath.so), which is not installed by default in most Linux distributions. |
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. This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium.
More information about the SBGrid Consortium is available at https://sbgrid.org
Report software bugs: sbgrid.org/bugs |
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