SBGrid Newsletter: July 2025

Dear Consortium Members and Affiliates,

Our July update includes news about our new strategic partnership with Instruct-ERIC, a profile on SBGrid member Emina Stojković, preparations for our next webinar season, a software push with 27 updates and nine new titles, six new members to welcome, and two publication highlights.

We're excited to announce a new strategic partnership with Instruct-ERIC, a pan-European distributed research infrastructure with a hub in Oxford, UK, to strengthen support for structural biology communities across Europe. Together, Instruct-ERIC and SBGrid will support European members through a range of joint activities, combining our strengths to build a more connected, sustainable, and responsive infrastructure for structural biology in the region of Europe. Learn more about this strategic collaboration: https://sbgrid.org/news/connecting_sbgrid-with-instruct_eric

Emina Stojković is the focus of our July member tale. She spoke with us from Northeastern Illinois University in Chicago where she has resumed marathon training, a helpful diversion from her years as an international student watching as civil war tore her home country apart. Today Stojković is exploring new frontiers in photoreception and signaling while seeking new opportunities to advance the careers of her undergraduate and master students after three NIH grant terminations. Read the full story: https://sbgrid.org/members/tale/drawn_to_the_light.

Next season's software webinar series is beginning to take shape. If there is a software title you'd like to hear more about, please reply to this email to let us know. To receive email reminders about upcoming webinars, please be sure to register for the series!

Registration here: https://sbgrid.org/webinars/#register

Oct 14: Alisia Fadini and Minhuan Li - Rocket

Nov 11: Hui Wang - TomoNet: A Streamlined Toolbox for High-Throughput CryoET STA and the 'Expand' Method for Lattice-Like Particle Picking

Additional dates coming soon!

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 autoPROC, AreTomo3, BCFtools, BioXTAS RAW, BUSTER, Cactus, ChimeraX, Cryo_fit2, drgnai, DIALS, IMOD, IPA, Julia, MMseqs2, OpenMM, ORCA, PDBFixer, POKY, RDKit, SAMtools, Schrodinger Suite, Scipion plugins, Topaz, Volume_Seg_Tool, Warp, and Xmipp, along wtih nine new titles: abismal, AITom, DenoisET, EMPOT, FoldBench, IntelliFold, PyCoAn, UGENE, and vina-CUDA. See Software Updates below for additional details.

Six new members joined in the month of July: Aleksandar Antanasijevic from École Polytechnique Fédérale de Lausanne, Anthony Pedley from University of Iowa, Baek Kim from Emory University School of Medicine, Derek Claxton from Vanderbilt University, and Baoyu Chen and Xiaofeng Qi from UT Southwestern Medical Center. Welcome to our newest members!

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 new IUCrJ article from SBGrid member Nikolaus Grigorieff that describes an in situ structure of the ribosome determined using knife cut cellular sections. Read more: https://medium.com/sbgrid-community-news/the-cutting-edge-of-cellular-microscopy-6d995d99e050

- Meharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a Nature Communications publication from the laboratory of Christopher Lima whose work helped to uncover how the cell’s nuclear gateway controls molecular traffic and regulate protein function, offering new insights into gene regulation and disease. Read more: https://medium.com/sbgrid-community-news/dual-role-of-the-nuclear-gatekeeper-47013dcb1b05

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 six new citations since our last reporting, from these current and former SBGrid members: 

David Jeruzalmi from City College of New York in Nucleic Acids Research: DnaB and DciA: mechanisms of helicase loading and translocation on ssDNA; Philip Kranzusch, Andrew Kruse, Josefina del Mármol from Harvard Medical School in Nature: A DNA-gated molecular guard controls bacterial Hailong anti-phage defence;

Holger Sondermann from Cornell University in Molecular and Cellular Biology: Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation in Pseudomonas aeruginosa; Edward Twomey from Johns Hopkins University School of Medicine in Nature Communications: Memantine inhibits calcium-permeable AMPA receptors; Dhrirendra Simanshu from Frederick National Laboratory for Cancer Research in Science with collaborators in Science: Molecular glues that facilitate RAS binding to PI3Kα promote glucose uptake without insulin; Stephanie Wankowicz and James Fraser from University of California, San Francisco in eLife: Expanding automated multiconformer ligand modeling to macrocycles and fragments.

abismal 0.3.0d is a tool for scaling and merging large X-ray crystallography diffraction datasets using stochastic variational inference and deep learning. The software implements approximate Bayesian inference methods specifically designed for processing data from advanced light sources. It supports NVIDIA CUDA acceleration and is currently under active development for handling large-scale crystallographic data processing workflows. Due to duplicate naming, look for this title as rs-station_abismal: https://github.com/rs-station/abismal

AITom 0.0.1 is an open-source platform for AI-driven cellular electron cryo-tomography analysis: https://github.com/xulabs/aitom.

DenoisET 0.1.0 is an implementation of the Noise2Noise algorithm specifically designed for cryoET data denoising that streamlines integration with AreTomo3 and provides automated tomogram selection for training and inference transition decisions to avoid overdenoising artifacts. It can operate during live data collection, either applying pre-trained models or training new 3D denoising models from scratch using CTF-deconvolved tomograms: https://github.com/apeck12/denoiset

EMPOT fbb781d is an algorithm designed for solving the partial alignment of cryo-EM density maps: https://github.com/artajmir3/EMPOT 

FoldBench 1.0 is a comprehensive all-atom benchmark for biomolecular structure prediction that spans proteins, nucleic acids, ligands, and six major interaction types. The benchmark includes 1,505 low-homology targets covering protein-protein, antibody-antigen, protein-ligand, protein-peptide, protein-RNA, and protein-DNA interfaces, plus monomeric structures for proteins, RNA, and DNA. It provides standardized evaluation metrics and a leaderboard comparing major structure prediction models, including AlphaFold 3, Boltz-1, Chai-1, HelixFold 3, and Protenix, across different molecular interaction types: https://github.com/BEAM-Labs/FoldBench.

IntelliFold 0.1.4 is a controllable foundation model for general and specialized biomolecular structure prediction that supports proteins, nucleic acids, and their complexes: https://github.com/IntelliGen-AI/IntFold.

PyCoAn 0.3 is a Python-based framework for analyzing electron microscopy data within a unified, Matlab-like environment. The package provides a distinctive correlation-based docking methodology that uses cross-validation to define confidence intervals for solutions. It includes tools for denoising, segmentation, and pattern recognition, and is designed to integrate numerous external data-processing packages through a single interface: https://github.com/pyCoAn/distro.

UGENE 52.1, from Unipro, is a free, cross-platform software designed to help molecular biologists manage, analyze, and visualize their data. It combines popular bioinformatics tools in one user interface, supports many biological data formats, can fetch data from remote sources, offers visualization for genome sequences, NGS data, sequence alignments, phylogenetic trees, and 3D structures. Its algorithms are optimized for speed and can use multiple processor cores. UGENE also lets users build and run reusable analysis workflows on their own computers or on high-performance computing systems: https://ugene.net/. 

vina-CUDA 2.1 is based on Vina-GPU 2.1, QuickVina2-GPU 2.1, and QuickVina-W-GPU 2.1; it optimizes its core algorithms through deep utilization of GPU hardware features to improve docking speed: https://github.com/HPCLab-933/Vina-CUDA

autoPROC 20250717 includes specific checks for problematic XDS versions (20240712-20250409) that give poor results, adds a new tool for creating MTZ appendices with metadata, and introduces ana_correct for creating plots from XDS output. The release also features improved ice-ring handling, better support for PAD detectors including Pilatus4 HDF5 datasets, and enhanced multi-crystal scaling capabilities with automatic exclusion of poor image ranges.

https://www.globalphasing.com/autoproc/ReleaseNotes/ReleaseNotes-autoPROC_snapshot_20250717.txt

AreTomo3 2.2.2 improves and fixes bugs in CTF estimation, making it more robust, particularly for datasets collected at low defocus settings with Volta phase plates. This version allows users to disable CTF estimation and correction by setting -Kv to 0, fixes bugs in tilt axis refinement while enabling users to disable it, and enables -FmDose command line parameter to supersede mdoc file values: https://github.com/czimaginginstitute/AreTomo3/releases/tag/v2.2.2. 

BCFtools 1.22 includes support for matching lines by ID, adds Fisher's exact test support in filtering expressions, and introduces a new -v/--verbosity option for all commands. The release includes numerous bug fixes across multiple commands including improved sample handling in bcftools call, enhanced gVCF processing in consensus, and better merge handling for indel-only records and symbolic alleles:

https://github.com/samtools/bcftools/releases/tag/1.22.

BioXTAS RAW 2.3.1 is a bug fix release that addresses several compatibility issues and processing errors: https://bioxtas-raw.readthedocs.io/en/latest/changes.html.

BUSTER 20250717 includes support for partial-occupancy aware bulk solvent masking via the new "aB_solmsk" tool with different masking algorithms, a new "aB_phase_from_model" tool for computing phases from heavy atom models, and a completely rewritten "rhofit2" interface for ligand fitting with improved assessment and real-space refinement capabilities. The release also adds a new "-ldir" command-line argument for simplified restraint dictionary provision and includes various improvements to Grade2 for better handling of salts, force field helpers, and quantum chemical methods: https://www.globalphasing.com/buster/ReleaseNotes/ReleaseNotes-BUSTER_snapshot_20250717.txt.

Cactus 2.9.9 introduces (prototype) FastGA support for Progressive Cactus via the --fastga option, updates Toil to version 8.2.0, and addresses various bugs including GPU functionality with Singularity binaries, proper command generation in cactus-update-prepare, early detection of empty FASTA input, correct handling of the --restart flag in cactus-minigraph, rare make errors related to bin directory creation, and VCF construction crashes with incomplete reference contigs: 

https://github.com/ComparativeGenomicsToolkit/cactus/releases.

ChimeraX 1.10 includes Boltz structure prediction for machine-learning-based prediction of proteins, nucleic acids, and small-molecule ligands, Profile Grids for summarizing sequence alignments as position-by-residue-type grids, and trajectory measurement plotting capabilities. Additional features include MUSCLE v5 sequence alignment, LAMMPS trajectory support, thermal ellipsoid visualization, and enhanced cavity finding tools with parameter adjustment options: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog.

drgnai 0.3.3-beta completes the implementation of tilt-series subtomogram averaging with CTF-based tilt selection, proper parameter validation, and interactive particle filtering capabilities. This release adds automatic mixed precision training support for up to 2x runtime speedup, includes improved documentation, and PyTorch compatibility fixes: https://github.com/ml-struct-bio/drgnai/releases/tag/0.3.3-b

DIALS 3.25.0 introduces significant enhancements for multi-crystal processing, including a substantially updated dials.import_xds program that converts XDS INTEGRATE.HKL and XDS.INP files to DIALS format for use with xia2.multiplex. The release adds unmerged mmcif file generation for data deposition, and improved logging and performance for large datasets: https://github.com/dials/dials/releases/tag/v3.25.0

IMOD updates 5.1.3 and 5.2.2b were pushed. 

• 5.1.3 includes numerous bug fixes addressing critical issues in the BatchRunTomo interface for cluster environments, image drawing problems on Mac with Qt6, and crashes in various modules including Beadtrack, meshing, and slicer operations. The update also resolves cluster-related problems with process pausing, resuming, and reconnection, and adds improvements to the Align Frames and Fine Alignment interfaces: https://bio3d.colorado.edu/imod/changes5.1.x.html
• 5.2.2b adds an option to Imodmop for filling inside contours with gaussian noise and enabling 3dmod to read shared memory files created with Manageshrmem. It fixes issues with cluster process management, including problems with pausing, resuming, and reconnecting to processes, and improves the the Align Frames and Fine Alignment interfaces: https://bio3d.colorado.edu/ftp/latestIMOD/recentChanges.txt.

IPA 1.2.1  is now available.

Julia 1.11.6 includes new features, some language changes, compiler/runtime improvements, changes in command line and multithreading, and new library features: https://github.com/JuliaLang/julia/blob/v1.11.6/NEWS.md.

MMseqs2 17-b804f is mostly a bug fix release. Highlights include usability improvements in MMseqs2-GPU and a fix for a common crash in the prefilter that was affecting many clustering runs: https://github.com/soedinglab/MMseqs2/releases. 

OpenMM 8.3.0 adds several new or updated force fields including Amber ff19SB, CHARMM36 2024, and CHARMM polar 2023 versions. This release introduces DPDIntegrator for Dissipative Particle Dynamics simulations, CustomVolumeForce for periodic box-dependent forces, and enhanced barostat capabilities for instantaneous pressure computation. It also includes support for constant pH simulations and improved PDBx/mmCIF file loading with bond information for heterogens: 

https://github.com/openmm/openmm/releases/tag/8.3.0.

ORCA 6.1.0 has overall performance and stability improvements and fixes. Several magnetic properties are now available for high-level ab-initio methods. Higher order molecular properties like the Raman Intensities can now be computed analytically.

PDBFixer 1.11 includes bug fixes and a new feature allowing users to specify the Platform for calculations. The release adds hydrogens to caps, fixes exceptions with unknown residues, and provides platform selection capabilities for improved computational control: https://github.com/openmm/pdbfixer/releases/tag/v1.11.

Phenix was updated to include the Cryo_fit2 module: https://phenix-online.org/documentation/tutorials/cryo_fit2_install.html.

POKY 20250618 is now available. 

RDKit 2025.03.4 includes enhancements to stereoisomer enumeration with C++ implementation, improved CIP labeling that resolves "easy" stereo centers first and is now interruptible, and support for bond-only stereogroups from Python. This release fixes critical issues including multithreaded mol reader hangs, segmentation faults in molecule embedding, and problems with wiggly bonds in stereoisomer enumeration.

https://github.com/rdkit/rdkit/releases/tag/Release_2025_03_4.

SAMtools 1.22.1 is a security and bug fix release that addresses a critical use-after-free vulnerability in samtools mpileup -a that could occur when all alignments for a reference start at the same position. This version bundles htslib-1.22.1 and htscodecs v1.6.4, which fix a potential buffer overflow on invalid CRAM inputs and failures with very long alignment records in CRAM version 3.1:

https://github.com/samtools/samtools/releases/tag/1.22.1.

Schrodinger Suite 2025-2 introduces a new Crystal Structure Prediction interface for ranking Z'=1 crystal polymorphs, a FEP+ Pose Builder workflow for automated ligand alignments, and optimized Glide for faster docking. This release also expands protein degrader modeling capabilities and adds machine learning-based T-cell receptor structure prediction for enhanced biologics research: 

https://www.schrodinger.com/release-download/#whats-new.

Scipion plugins 3.7.1 includes new cryoDRGN and Modelangelo plugins and updates to the RelionTomo and XMIPP (v3.25.06) plugins.

https://github.com/scipion-em/scipion-em-cryodrgn 

https://github.com/scipion-em/scipion-em-modelangelo 

https://github.com/scipion-em/scipion-em-reliontomo 

https://github.com/I2PC/scipion-em-xmipp/releases/tag/v3.25.06.0-Rhea

Topaz 0.3.11 is now available. 

Volume_Seg_Tool 0.9.0 is the first public release ready for production use and includes comprehensive functionality for volume segmentation, though additional testing is still needed to ensure the installation script works robustly across different systems: https://github.com/fgdfgfthgr-fox/Volume_Seg_Tool/releases/tag/v0.9.1.

Warp v2.0.0dev34 includes a number of minor fixes and updates as well as additional  documentation and a --strict option to ts_import: 

https://github.com/warpem/warp/compare/v2.0.0dev33...v2.0.0dev34  

Xmipp 3.25.06 includes updated environments for DeepLearningToolkit with new features for thirteen protocols, bug fixes for eight protocols, and one new protocol: Compute Likelihood: https://i2pc.github.io/docs/Releases/Releases-xmipp-program/index.html#rhea 

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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