SBGrid Newsletter: June 2026
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Dear Consortium Members and Affiliates,
For our June updates, we have a few annual renewal reminders, a member tale featuring SBGrid member Dhirendra Simanshu from the Frederick National Laboratory for Cancer Research, a July software webinar on Ais and Pom, a software push with 15 updates and three new titles, eight new members to welcome, two upcoming events hosted by our partners at Instruct-ERIC, and student publication highlights featuring work from the laboratories of Alexandra Trkola, Douglas Reese and Bil Clemons.
Tomorrow (July 1) marks the annual renewal date for all SBGrid members and the date that our shared licenses for PyMOL and Schrodinger renew and our Geneious license expires. A few notes to keep things running smoothly during this transition period: -
Renewal Invoices: Annual invoices are out and we are grateful to all who are able to process these payments quickly. Credit card payments are the surest way to ensure a speedy delivery, but we also accept POs, wire/ACH transfers, and from internal Harvard groups, 33-digit billing codes.
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PyMOL (for nonprofit members): the license file for the July 1 renewal is already available through the SBGrid Installation Manager. If you get a message that the PyMOL license is expired, please update to the latest version of PyMOL and the error should resolve. If updating PyMOL via the installation manager does not pick up the new license file, please email us at bugs@sbgrid.org and include the output of the `pymol –help` command.
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Schrödinger (for nonprofit groups that have opted in): Alongside the Schrödinger license renewal, we are updating the operating system of the license server. You may encounter a short interruption in access on June 30th while these updates are completed.
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Geneious: As previously communicated, Geneious has discontinued their shared license model, and SBGrid’s license will expire today (June 30th). Please contact Geneious directly for continued access https://www.geneious.com/, or try this open source alternative some of our users have recommended: https://www.vectorbee.com/en/.
Our June member tale features Dhirendra Simanshu, who spent the last 12 years building the structural biology program at the Frederick National Laboratory for Cancer Research RAS Initiative and leading research on the KRAS protein. Simanshu's inspiration to transform a chemical glue, which strengthened KRAS-PI3Ka interaction, into a breaker to disrupt it, is now in a phase 1 clinical trial with encouraging results. [Read More].
Join us July 14th for the last in this season's software webinars with a presentation on the cryo-ET tools Ais and Pom from Mart Last of the Allegretti group at MRC Laboratory of Molecular Biology.
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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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 -- AlphaFold3, AlphaPulldown, ChemEx, cryoDRGN, DeepDeWedge, EMReady2, OpenForceField Toolkit, MassiveFold, ModelAngelo, PRODIGY, PowerFit, protein-quest, Scipion, STOPGAP, and TOMOMAN --- along with three new applications: CryoROLE, CryoZeta, and warpylib. See Software Changes below for complete details.
Eight new members joined in the month of June: John Brognard from SUNY Upstate Medical University, Jose-Jesus Fernandez from Health Research Institute of Asturias (ISPA), Veit Hornung from Ludwig Maximilians Universität München, Jaekyung Hyun from Sungkyunkwan University, Ruben Sanchez-Garcia from IE University, Jae Yang from St. Jude Children's Research Hospital, The Structural Biology Core led by Jason De La Cruz at Memorial Sloan-Kettering Cancer Center, and Carmen San Martin and José Maria Valpuesta from Centro Nacional de Biotecnologia,
Welcome to our newest members! |
Upcoming events from our partners at Instruct-ERIC |
Member Publication Highlights |
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 the laboratories of Douglas Reese and Bil Clemons of California Institute of Technology that describe the cryo-EM structure of a bacterial metalloid pump and the mechanisms that could offer more insight into ridding environments of toxic metalloids. [Learn more.]
- Meharry Medical College student Mudia Ikoba highlights a publication from SBGrid member Alexandra Trkola and colleagues at the University of Zurich in which the authors propose including people living with HIV in vaccination trials to gain a deeper understanding of the immunologic response to broadly neutralizing antibody-based HIV vaccines. [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: 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).
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CryoROLE is a python package designed to analyze the particle distribution of the relative orientation between two independently refined domains of a biological complex. The landscape is represented in angular (real) space. Version 2026061.
https://github.com/yifancheng-ucsf/cryorole
CryoZeta is a de novo macromolecular structure modeling tool that integrates cryo-EM density information with a diffusion-model-based structure prediction pipeline. Version 20260612.
https://github.com/kiharalab/CryoZeta
warpylib is a Python library replicating core functionality from WarpLib, a C# framework for cryo-electron tomography data processing, built on PyTorch for GPU acceleration and automatic differentiation. Version 1.0.0
https://github.com/warpem/warpylib
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AlphaFold3 3.0.3 improves performance for large inputs, including much faster confidence JSON serialization, and fixes issues affecting Jackhmmer/Nhmmer flag handling, glycan atom handling, chain descriptions, and typing checks.
https://github.com/google-deepmind/alphafold3/releases/tag/v3.0.3
AlphaPulldown 2.4.1 adds mmseq precomputed enrichment support, and updates AlphaFold3 support to Tokamax v3.0.2.
https://github.com/KosinskiLab/AlphaPulldown/releases/tag/2.4.1 AlphaPulldown 2.5.0 updates the AlphaFold3 backend to AlphaFold3 v3.0.3 and adds support for RTX PRO 6000 / Blackwell GPUs, resolving crashes seen on those systems. The AlphaFold2 backend is unchanged aside from a NumPy 2 compatibility fix, with AF2 monomer GPU inference re-validated.
https://github.com/KosinskiLab/AlphaPulldown/releases/tag/2.5.0
ChemEx 2026.06.0 adds MCMC posterior sampling for estimating fitted-parameter uncertainty, with posterior summaries, samples, correlations, diagnostics, credible intervals, and a PDF report. This release also standardizes the output layout for Monte Carlo, bootstrap, and MCMC uncertainty analyses.
https://github.com/gbouvignies/ChemEx/releases/tag/2026.06.0
cryoDRGN 4.3.0 adds an end-to-end interactive dashboard web application for visualizing cryoDRGN results plus a browser-based command builder for assembling cryoDRGN commands. It also improves parse_pose_csparc by detecting -D resolution from .cs files when available and adds eval_vol support for abinit reconstruction outputs.
https://github.com/ml-struct-bio/cryodrgn/releases/tag/4.3.0
DeepDeWedge 20260602 is based on commit 0720756, is built with Blackwell GPU support, and includes some bug fixing related to aretomo3 tomograms.
https://github.com/MLI-lab/DeepDeWedge/commits/master/
EMReady2 ea8c5b6 is now available as a separate title. It was previously included in SBGrid under the title EMReady (versions 2.X); however, the original code was moved from the developer website to GitHub (without versioning) along with recent commits. Recent changes include compatibility updates for torch and mamba, with a runtime environment upgraded from torczh 2.3 to torch 2.4.1, added Gaussian post-processing, and simplified installation with a move from a shell-script to an installable Python package workflow in a conda environment.
OpenForceField Toolkit 0.18.1 fixes loading of N-terminal, protonated, and disulfide-bonded cysteine residues in Topology.from_pdb.
https://github.com/openforcefield/openff-toolkit/releases/tag/0.18.1
MassiveFold 1.8.2 includes minor bug fixes.
https://github.com/GBLille/MassiveFold/releases/tag/v1.8.2
ModelAngelo 1.0.18 includes minor changes.
https://github.com/3dem/model-angelo/releases/tag/v1.0.18
PRODIGY 2.4.0 adds multi-model support and multiprocessing, which improves handling of larger or multi-model prediction inputs.
https://github.com/haddocking/prodigy/releases/tag/v2.4.0
PowerFit 5.0.2 is a minor bug fix update.
https://github.com/haddocking/powerfit/releases/tag/v5.0.2
protein-quest 1.4.0 adds support for CIF/CIF.GZ conversion, resolution-based filtering, and selecting the best structure per UniProt accession, making it easier to search, download, convert, and filter protein structures.
https://github.com/haddocking/protein-quest/releases/tag/v1.4.0
Scipion 3.11.6 incorporates a scipion-em-motioncorr 4.0.1 plungin, which brings support for MotionCorr3 1.2.4, and adds the scipion-em-xmipptomo plugin.
STOPGAP 0.7.5 updates how template matching is parallelized. Rather than splitting the input tomogram by the number of cores, an input tilesize is given. The tilesize is essentially the target size of the tile to be spliced back into the output maps. The actual extraction size is tilesize + template size, rounded down to generate equally sized tiles. Parallelization is then between tiles and angles. Additional bug fixes are also included in this release.
TOMOMAN 0.9.1 adds ARCTiC, for the automated removal of bad tilts, new functions to export STOPGAP projects to WarpTools, IsoNet, and IsoNet2 for denoising and missing-wedge compensation, MemBrain-Seg for membrane segmentation, MUST for 3D CTF-corrected tomogram reconstruction, MotionCor3 for frame alignment, and PyTOM MatchPick for template matching.
https://github.com/wan-lab-vanderbilt/TOMOMAN/releases/tag/0.9.1
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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
This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium. |
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