SBGrid Newsletter: September 2025

Dear Consortium Members and Affiliates,

Our September monthly update includes a profile of Gira Bhabha from Johns Hopkins University, a reminder of the October software webinar introducing ROCKET, seven new members to welcome, a software push with 21 updates and 13 new titles, notes from our software team about MacOS Tahoe and Apple's plans to phase out support for Intel-based Macs, and two member publication highlights.

Our member tale for October features Gira Bhabha, who had plans for degrees in psychology and English Literature, then Veterinary medicine, before finding her home in the lab where microscopy caught her eye. Now at Johns Hopkins University, Bhabha's laboratory is joined with that of Damian Ekiert, her partner in science and in life, where she studies MCE proteins in tuberculosis and the interactions between microsporidia parasites and host cells. Read the full story: https://sbgrid.org/members/tale/probing_microbes 

On Tuesday, October 14th we str kicking off our software webinar series with Alisia Fadini (University of Cambridge/Columbia University) and Minhuan Li (Center for Computational Mathematics, Flatiron Institute) introducing ROCKET. Additional details below.

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

October 14:  Alisia Fadini and Minhuan Li - Rocket 

November 18: Hui Wang - TomoNet

More dates coming soon

April 14: Jose Luis Vilas - scipionTomo

May 12: Jarrett Johnson - PyMOL

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 21 titles - AlphaPulldown, Boltz, ChemEM, ColabDesign, cryoDRGN, EMReady2, GROMACS, HADDOCK, NMRFxAnalyst, NMRFxStructure, PowerFit, PyTom-Match-Pick, R, RDKit, RFDiffusion, Scipion, SSDraw, Starparser, Topaz, Volume_Seg_Tool, and Warp - along with 13 new applications: AlphaBridge, ARCTIC-3D, BindCraft, cryoTIGER, DeepRank-GNN-esm, DockQ, HADDOCK3, OpenFreeEnergy, OpenForceField Toolkit, PolNet, PRODIGY, prodigy-lig, and TomoStarPy. 

See Software Changes below for complete details.

Seven new members joined since our last report: Tyler Beyett at Emory University School of Medicine, Terje Dokland at the CryoEM Microscopy Facility from University of Alabama at Birmingham, Pierre Gönczy from École Polytechnique Fédérale de Lausanne, Wenyi Li from La Trobe University, Cristina Vega from Margarita Salas Center for Biological Research, and Susanne Kassube and Gregor Weiss from University of Zurich. Welcome to our newest members!

MacOS 26 Tahoe: Our team is testing macOS Tahoe and one important issue to note is that XQuartz-based OpenGL acceleration is partly broken. This issue causes problems with applications like Coot. Most other applications behave as expected, but please let us know at bugs@sbgrid.org if you encounter problems or have questions.

Apple sunsetting support for Intel-based Macs: macOS 26 Tahoe is the last release that will support Intel-based Macs. Apple also announced that the rosetta2 framework that allows ARM64 Macs to run x86_64 executables is scheduled for removal in macOS 28, after which programs that can't be updated for ARM64 will stop working on macOS.

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:

- Caltech doctoral student Vida Storm Robertson highlighted a publication from Jens Meiler, from Vanderbilt University, who describes using Rosetta to design antibiotic peptides called lanthipeptides with antibiotic properties. [Read more]

- Meharry Medical College Ph.D. graduate KeAndreya Morrison's highlight features a publication from the laboratory of William Clemons Jr. from California Institute of Technology that reveals how the ArsA enzyme reshapes itself to capture and expel toxic arsenic, providing a structural blueprint for microbial survival. [Read 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.

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.

SBGrid's eLife paper received nine new citations since our last reporting, from these SBGrid members: 

Jue Chen from The Rockefeller University in PNAS: Structurally diverse viral inhibitors converge on a shared mechanism to stall the antigen transporter TAP; Jonathan Clinger from Baylor University in biomolecules: Multi-Temperature Crystallography of S-Adenosylmethionine Decarboxylase Observes Dynamic Loop Motions; Eric Fischer from Dana Farber Cancer Institute in Nature Communications: Structural basis of VCP-VCPIP1-p47 ternary complex in Golgi maintenance; M. Gordon Joyce from the Walter Reed Army Institute of Research in mBio:

First-generation N-terminal domain supersite public antibodies retain activity against Omicron-derived lineages and protect mice against Omicron BA.5 challenge; João Rodrigues from Schrödinger, Inc. in FEBS Letters: Towards better structural models from cryo-electron microscopy data with physics-based methods; Dhirendra Simanshu from Frederick National Laboratory for Cancer Research in Science: Structural basis for LZTR1 recognition of RAS GTPases for degradation; Edward Twomey from Johns Hopkins University School of Medicine in Nature: Delta-type glutamate receptors are ligand-gated ion channels; Pedro José Barbosa Pereira from University of Porto in Chemical Science: Engineering ultrapotent trivalent anticoagulants through hybridisation of salivary peptides from multiple haematophagous organisms; and Ji-Joon Song from Korea Advanced Institute of Science and Technology in Molecular Cell: Structural determinants of DANGEROUS MIX 3, an alpha/beta hydrolase that triggers NLR-mediated genetic incompatibility in plants.

AlphaBridge 4c3352f is a script that uses AlphaFold3 output to provide different plots and files useful for the identification of interacting interfaces.

https://github.com/PDB-REDO/AlphaBridge 

ARCTIC-3D 0.5.1 is a software for data-mining and clustering of protein interface information that retrieves existing interaction data from the PDBE graph database and groups similar interfaces in interacting surfaces. This tool checks input (UniProt ID, FASTA file, or PDB file), projects interfaces onto selected PDB structures, calculates dissimilarity, and applies hierarchical clustering algorithms. It identifies binding surfaces characterized by hotspot residues that are always present and other amino acids that appear at interfaces intermittently.

https://github.com/haddocking/arctic3d

BindCraft 1.5.2 is a small bug fix update.

https://github.com/martinpacesa/BindCraft/releases/tag/v1.5.2

cryoTIGER 5423d86 (Tilt Interpolation Generator for Enhanced Reconstruction) in cryo-electron tomography is a computational workflow leveraging a deep learning-based frame interpolation to generate intermediate tilt images. By interpolating between tilt series projections, cryoTIGER improves angular sampling, leading to enhanced 3D reconstructions, more refined particle localization, and improved segmentation of cellular structures.

https://github.com/turonova/cryoTIGER 

DeepRank-GNN-esm 0.2.2 is a graph neural network framework for scoring protein-protein interfaces that incorporates ESM-2 language model embeddings. This tool provides both a command-line interface for direct complex scoring and a Python framework for custom applications, generating predictions of interface quality (fnat values) from PDB structures. It includes pre-trained models and supports both CPU and GPU environments for analyzing protein-protein binding interfaces.

https://github.com/haddocking/deeprank-gnn-esm

DockQ 2.1.3 is a quality measure for protein, nucleic acid, and small molecule docking models that provides a single continuous scoring metric. This tool evaluates docking poses by computing interface RMSD, ligand RMSD, fraction of native contacts, and an overall DockQ score with interpretable quality thresholds. It supports automatic chain mapping optimization, handles multi-interface complexes, and can be used both as a command-line tool and Python module.

https://github.com/bjornwallner/DockQ

HADDOCK3 2025.8.0 is a new open source and modular version of HADDOCK

https://github.com/haddocking/haddock3/releases/tag/2025.8.0 

OpenFreeEnergy 1.6.0 is a Python package for executing alchemical free energy calculations. It provides robust, permissively licensed open-source tools for molecular simulation in the drug discovery field, enabling users to easily plan and execute alchemical free energy calculations.

https://omsf.io/programs/projects/openfreeenergy/

OpenForceField Toolkit 0.17.0 is a Python toolkit for the development and application of modern molecular mechanics force fields, leveraging direct chemical perception and rigorous statistical parameterization methods. It provides tools for utilizing SMIRKS Native Open Force Field (SMIRNOFF) force fields. The toolkit also includes capabilities for direct chemical environment perception and manipulation, aiding in the accurate representation of molecular systems.

https://github.com/openforcefield/openff-toolkit

PolNet 1.0.0 is a Python package for generating synthetic datasets of the cellular context for Cryo-Electron Tomography. The core simulation capabilities for biological structures include simulation of cellular membranes with spherical, ellipsoidal, and toroidal geometries for membranes, simulation of cytoskeletal structures including actin filaments and microtubules with helicoidal geometry for filaments; 

Simulation of globular protein clusters using Self-Avoiding Walk on Lattice (SAWLC) networks for protein complexes, and simulation of membrane-bound protein complexes for membrane proteins.

https://github.com/anmartinezs/polnet/releases/tag/v1.0.0 

PRODIGY 2.3.0 (PROtein binDIng enerGY prediction) predicts the binding affinity of protein–protein complexes from their 3D structure. It implements a predictive model based on intermolecular contacts and properties derived from non-interface surface.

https://github.com/haddocking/prodigy/releases

prodigy-lig 1.1.3 (PROtein binDIng enerGY prediction - LIGands) is a structure-based method for the prediction of binding affinity in protein-small ligand (such as drugs or metabolites) complexes.

https://github.com/haddocking/prodigy-lig/releases 

TomoStarPy 20250912 is a collection of Python scripts for manipulating Relion tomo STAR files and performing various cryo-electron tomography data processing tasks. The toolkit includes utilities for CTF fitting on tilt series, dose correction, coordinate transformations, particle filtering, and format conversions between different software packages including emClarity, IMOD, and Warp. It also provides visualization tools for particle editing and placeback operations for structural analysis in tomographic reconstructions.

AlphaPulldown 2.1.2 introduces AlphaFold3 data pipeline support for generating compatible feature files from FASTA sequences, enables mixing of AlphaFold2 and AlphaFold3 features in the same prediction run, and includes bug fixes for MSA pairing with AF3 backend and issues affecting sequence pairing accuracy. The update also provides support for all AlphaFold3 feature types including proteins, DNA, RNA with PTMs, and ligands.

https://github.com/KosinskiLab/AlphaPulldown/releases/tag/2.1.2

Boltz 2.2.1 includes multiple bug fixes and improvements, addressing issues with PoseBustersPotential bounds, input filtering for affinity calculations, and tensor padding for static sizes. This release also fixes problems with bf16 dropout, bias repeat handling when multiplicity > 1, and resolves a NoneType error in inference pocket constraints.

https://github.com/jwohlwend/boltz/releases/tag/v2.2.1

ChemEM 0.06 introduces user-supplied difference maps for docking, protonation state assignment using di-Morpholite, and support for multiple ions (Ca, Cl, Co, Cu, Fe, K, Mg, Mn, Na, Ni, Zn) in scoring functions. This update also adds hold-fragments functionality for restraining specific atoms during post-processing, system ligands integration, SASA-based surface residue definition, and support for different Amber force fields for ion parameters and implicit solvent models.

https://chemem.topf-group.com/ChemEM_Documentation_v0.3.pdf

ColabDesign 1.1.3 fixes a sampling temperature parsing bug.

https://github.com/sokrypton/ColabDesign/releases/tag/v1.1.3

cryoDRGN 3.5.1  is a patch release that introduces the --force-ntilts option for filtering particles based on available tilts and improves robustness for tilt-series indexing in interactive filtering. This release also introduces scatterplots as the default output for plot_classes and improves .star file formatting with RELION-style column numbering. Landscape analysis outputs also now consistently uses 1-indexing.

https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.5.1

EMReady2 2.3 sets the voxel size of the EMReady2-processed map to be consistent with that of the input map as the default option, and provides interp.py to allow users to freely perform interpolation operations on the map.

GROMACS 2025.3 is a bug-fix release that resolves critical issues with AWH free-energy lambda coordinates and bias sharing functionality that could cause incorrect simulation behavior. This update includes numerous portability improvements for SYCL, ROCm 7, and CUDA 13 builds, along with fixes for GPU domain decomposition reporting and MPI library linking issues.

https://manual.gromacs.org/current/release-notes/2025/2025.3.html

HADDOCK 2.5 increased some array size parameters in the provided CNS code, added support for pyro-glutamic acid (PCA), modified analysis to write stage-specific CNS average job files, simplified CNS execution scripts, and added check of min/max coordinates for consistency with the PDB format.

https://www.bonvinlab.org/software/haddock2.4/changes/ 

NMRFxAnalyst 11.4.30 is available.

https://github.com/nanalysis/nmrfx/releases/tag/v11.4.30

NMRFxStructure 11.4.30 is available.

https://github.com/nanalysis/nmrfx/releases/tag/v11.4.30

PowerFit 3.0.5 delivers significant GPU performance improvements, with processing 2x faster than v3.0.3 and 1.5x faster than v3.0.4 for rigid body fitting of atomic structures in cryo-EM density maps. The update migrates from GpyFFT to VkFFT, resulting in substantially improved rotation speeds on GPU hardware while maintaining similar CPU performance.

https://github.com/haddocking/powerfit/releases/tag/v3.0.5

PowerFit 3.0.6 features improved GPU and CPU performance with significant speed improvements across all processing modes. Users can now disable the progress bar with --no-progressbar for additional speed gains, and the release includes new instructions for running on Intel integrated graphics for improved energy efficiency.

https://github.com/haddocking/powerfit/releases/tag/v3.0.6

PowerFit 3.1.0  adds a new `--report` feature that generates an interactive HTML report with Mol* visualization for fitted models, enhancing the analysis and presentation of rigid body fitting results for atomic structures in cryo-electron microscopy density maps.

https://github.com/haddocking/powerfit/releases/tag/v3.1.0

PyTom-Match-Pick 0.11.0  introduces several significant changes including absolute path storage for improved job portability, enhanced Relion5 compatibility with automatic binning and pixel size tracking, and improved handling of multi-data-block STAR files. This update also restructures CTF data handling and includes various bug fixes.

https://github.com/SBC-Utrecht/pytom-match-pick/releases/tag/0.11.0

R 4.4.2 includes over 500 new packages driven mainly by updates to the Seurat family of packages. New additions include the Azimuth application package. The default SBGrid R version 4.4.2, now contains over 1500 packages.

RDKit 2025.03.6 includes new CDX support for FileParsers and ChemDraw integration to SWIG, plus a useRingTemplates option for generateDepictionMatching2DStructure. This release fixes several critical issues including nondeterministic GETAWAY descriptors, incorrect canonicalization in CXSMILES generation, and memory allocation problems in PubChem shape code. It includes better error handling for parse failures, fixes for drawing functionality, and conformer canonicalization.

https://github.com/rdkit/rdkit/releases/tag/Release_2025_03_6

RFDiffusion 20250912 is now available.

https://github.com/RosettaCommons/RFdiffusion

Scipion 3.7.1 updates the Scipion core to the latest version (scipion-em@3.10.2, scipion-pyworkflow@3.11.2, scipion-app@3.8.3). Note that we've kept the version name “3.7.1” in SBGrid since the recent updates were minor (bug-fixing and hot-fixes).

SSDraw 2.0 adds amino acid sequence cropping functionality for protein secondary structure images with new CLI commands. The package now includes `ssdraw single` for individual sequences and `ssdraw multi` for multiple sequence alignments.

https://pypi.org/project/SSDraw/

Starparser 1.60 fixes a bug related with option –plot_orientations encountered in v1.58. No available release notes.

Topaz 0.3.14 and 0.3.16 are now available.

https://github.com/tbepler/topaz/releases/tag/v0.3.14

https://github.com/tbepler/topaz/releases/tag/v0.3.16

Volume_Seg_Tool 0.10.2 includes a more accurate and faster pixel reclaim algorithm in instance segmentation and a potentially more robust installation script.

https://github.com/fgdfgfthgr-fox/Volume_Seg_Tool/releases/tag/v0.10.2

Warp v2.0.0dev36 includes a number of bug fixes. 

https://github.com/warpem/warp/compare/v2.0.0dev35...v2.0.0dev36

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.

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