SBGrid Newsletter: June 2025

Dear Consortium Members and Affiliates,

As we look ahead to July with summer in full swing and a shift in some activites, our monthly SBGrid update includes a reminder about annual renewals, a link to our latest webinar recording, a software push with 21 updates and nine new titles, six new members to welcome, a note from our technical team about updating PyMOL, and two publication highlights.

It's renewal season at SBGrid, with a common anniversary date of July 1 for all member labs and institutions. Please let us know if there are any changes to the number of labs (non-profit) or users (for-profit) at your institution. Non-profit labs can also opt in for access to BioGrids ($600/lab), a stack of 700+ applications with collections for high-throughput sequencing, genomics, proteomics, visualization, and more. This software stack is also available for industry members. 

Many thanks to those who have already submitted renewal payments. We will reopen the credit card payment portal tomorrow (July1st). Please contact us at ar@sbgrid.org with any renewal changes, questions, or payment information.

We closed out our 2024-2025 Software Webinar Series with a presentation from Genki Terashi on DiffModeler & CryoREAD. If you missed us online, you can catch up on SBGridTV: https://www.youtube.com/watch?v=WmglqIYsJ20

Stay tuned for our 2025-2026 webinar lineup. If there is a software title you'd like to learn more about, please send your suggestions to events@sbgrid.org

Register for next season's webinar series

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 BioEmu, BLAST+, Boltz-1, ChimeraX, ColabFold, Cryo_fit, cryosparc-tools, Durin, Dynamo, GROMACS, LocScale, Modeller, NAMD, PowerFit, PyEM, Pytom-match-pick, QFit, SAMtools, Scipion, Topaz, and Vesicle-Picker, along with nine new titles: CCPEM-pipeliner, CryoTransformer, DiffModeler, GetContacts, LigandMPNN, RareFold, RosEM, Tomat, and VirtualIce.

Six new members joined in the month of June: Huanhuan Chen from University of Chicago, Mario Halic from St. Jude Children's Research Hospital, Sangwon Lee from Yale University School of Medicine, Mike Martynowyc and Monica Pillon from University at Buffalo, and Tianshu Xiao from Nanyang Technological University. Welcome to our newest members!

PyMol License for Non-profit Members

In conjunction with SBGrid's July annual renewals, our PyMOL license also renews. To get an updated license for PyMol using the SBGrid Installation Manager, please initiate a PyMOL update:

• GUI: click on the "Installed" tab on the left hand side, then click the "Update All" button. The new license will be included when you update.
• CLI: you can update like this: $ sbgrid-cli update pymol -y

Schrodinger updated the licensing framework in PyMOL this year and the older releases will no longer work. The following versions are supported with the new license and are enabled through June 2026:   

3.1.5.1   3.1.4.1   3.1.4   3.1.3.1   3.1.3   2.6.2   2.5.10.  

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 ACS Chemical Biology article from SBGrid member Andrew Gulick at University at Buffalo, who investigates the enzymes responsible for the non-ribosomal synthesis of iron transport molecules, siderophores. Read more: https://medium.com/sbgrid-community-news/bacteria-hunting-and-gathering-iron-c2c43f1fe79c

- Meharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a publication from the laboratory of SBGrid member Stefan Sarafianos at Emory University School of Medicine, who reports on how the E166V mutation in COVID-19 helps confer resistance to antiviral medications like Paxlovid. Read more: https://medium.com/sbgrid-community-news/new-study-uncovers-mechanisms-behind-covid-19-treatment-resistance-c34f381623f2

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 four new citations since our last reporting, from these SBGrid members: 

James Fraser of University of California, San Francisco in Science Advances: Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning; Jeffrey Holt from Boston Children's Hospital, along with a host of other SBGrid member contributors including Tianmin Fu of Ohio State University, Marcos Sotomayor from University of Chicago, and Shuan Rawson from Harvard Medical School, in Neuron: Structural and functional basis of mechanosensitive TMEM63 channelopathies; Robert Stroud from University of California, San Francisco in Nature Structural and Molecular Biology: Substrate recognition and allosteric regulation of synaptic vesicle glutamate transporter VGLUT2; and Dhirendra Simanshu  and Anna Maciag from Frederick National Laboratory for Cancer Research with colleagues from several other institutions in Science: BBO-10203 inhibits tumor growth without inducing hyperglycemia by blocking RAS-PI3Kα interaction.

CCPEM-pipeliner 1.3.0 is an integrated suite of software tools for processing single particle cryoEM data, from preprocessing raw image data through building and fitting atomic models: https://ccpem-pipeliner.readthedocs.io/en/latest/index.html

CryoTransformer 1.0.0 is a particle-picking framework using Residual Network (ResNet) and Transformer. It recognizes and extracts an abundance of true protein particles from the input micrographs while maintaining low false-positive rates: https://github.com/jianlin-cheng/CryoTransformer/

DiffModeler 2.3 a computational tool using a diffusion model to automatically build full protein complex structure from cryo-EM maps at 0-20A resolution: https://www.nature.com/articles/s41592-024-02479-0

GetContacts 20250531 is designed to dissect and visualize molecular interactions in proteins from various sources, including experimental structures (X-ray, NMR, Cryo-EM) and MD simulations: https://github.com/getcontacts/getcontacts

LigandMPNN 20250613 is a deep learning-based tool for designing protein sequences conditioned on atomic context, including ligands, DNA, RNA, and modified amino acids. It extends the capabilities of ProteinMPNN by allowing users to bias amino acid selection, fix specific residues, and design sequences for homo-oligomers:  https://github.com/dauparas/LigandMPNN

RareFold 20250606 is a tool for the structure prediction and design of proteins that include non-canonical amino acids. It supports 29 different rare, in addition to the 20 standard, amino acids. The package includes the EvoBindRare framework, which enables the de novo design of both linear and cyclic peptide binders with expanded chemical diversity, without requiring prior knowledge of the target's binding site: https://github.com/patrickbryant1/RareFold

RosEM 20250605 is a pipeline and Graphical User Interface (GUI) for cryo-EM model refinement that integrates Rosetta and Phenix. It automates testing different density weights and the use of restraints, currently implementing Rosetta's ⁠fastrelax protocol. It provides both command-line and GUI access for refining models against cryo-EM maps, selecting the best model based on FSC correlation: https://github.com/fmi-basel/RosEM

TomCat 0.2.1 is a web-based tool designed for cataloging and managing tomography data. It provides an intuitive interface to browse, view (including low-mag overviews and animations), annotate, and organize tomograms across multiple directories:  https://github.com/shahpnmlab/tomcat

VirtualIce 2.0.0 is a feature-rich half-synthetic cryoEM micrograph generator that uses buffer cryoEM micrographs with junk and carbon masked out as real background.

https://github.com/alexjnoble/VirtualIce

BioEmu 0.11.2 contains minor bug fixes:  https://github.com/microsoft/bioemu/releases/tag/v.0.1.12

BLAST+ 2.16.0 adds support to format searches involving filtered reads in blast_formatter_vdb and blast_vdb_cmd via the newly added include_filtered_reads option. This version also include numerous improvements and bugfixes: https://www.ncbi.nlm.nih.gov/books/NBK131777/

Boltz-1

• 2.0.3 introduces binding affinity prediction for protein-small molecule complexes, achieving a reported 1000x speedup compared to free energy perturbation methods. This version adds greater user control through contact, method, and structural template conditioning (including multimers). It also features improved modeling performance for antibodies and better ensemble generation with MD conditioning: https://github.com/jwohlwend/boltz/releases
• 2.1.1 introduces two novel kernels from NVIDIA for the triangular attention and triangular multiplication layers, with speed (2x speedier) and memory savings:https://github.com/jwohlwend/boltz/releases

ChimeraX 1.10-rc includes an enhanced command line history search allowing typed text to be found anywhere in the command (using Alt/Option key), and a new Thermal Ellipsoids GUI tool for displaying atomic anisotropic B-factors:

https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

ColabFold 1.5.5_2 integrates support for AlphaFold3 by adding JSON generation to its search pipeline and providing corresponding instructions: 

https://github.com/sokrypton/ColabFold/commits/main/

Cryo_fit 1.21.2-5419 was added as a module to Phenix: https://phenix-online.org/documentation/tutorials/cryo_fit_cmdline.html 

cryosparc-tools 4.7.0 includes a new automatic Micrograph Junk Detector, the ability to subset particle stacks based on statistics, improved reference based auto selection of 2D and 3D classes, and a number of performance improvements.

Durin 2023.10 addresses several compatibility issues, includes a fix for ⁠sprintf usage, and adds support for HDF5 version 1.12:  https://github.com/DiamondLightSource/durin/releases/tag/v2023-10

Dynamo 1.1.557 is available for Linux: https://www.dynamo-em.org/w/index.php?title=Downloads#Version_features 

GROMACS 2025.2 is a bug-fix release that resolves several issues. For ⁠mdrun, it fixes a crash in CUDA/HIP builds when domains are empty and another crash that could occur with a specific combination of position restraints, p-coupling, and OpenMP. For GROMACS tools, ⁠pdb2gmx now correctly parses PDB files with multiple cyclic chains, and ⁠gmx sorient fixes an out-of-bounds read affecting histogram output: https://manual.gromacs.org/current/release-notes/2025/2025.2.html

LocScale 2.3.1 is now available: https://github.com/cryoTUD/locscale/releases/tag/v2.3.1

Modeller 10.7 is a minor update with improved mmCIF output (supporting multiple chains, ligands, DNA/RNA, water, chemical components, restraints, and both Modeller and mmCIF IDs), the ability to read models and templates from BinaryCIF, and a change in the default ⁠Model.read() format to ⁠PDB_ANY:  https://salilab.org/modeller/release.html

NAMD 3.0.1 fixes bugs affecting pressure tensor calculation, colinear lonepair calculation, builds using CUDA 12.5 and higher when running in GPU-resident mode, and GPUAtomMigration for multi-GPU simulation and PME with multiple GPU devices. Colvars was also updated:  https://www.ks.uiuc.edu/Research/namd/3.0.1/announce.html 

PowerFit 3.0.2 introduces a major architectural update, migrating the package fully to Python 3. https://github.com/haddocking/powerfit/releases

PyEM 0.67 added a subgroup search option to subparticles.py:  https://github.com/asarnow/pyem/releases/tag/v0.67

Pytom-match-pick 0.9.0 has a better integration with pipelines using Warp for preprocessing, as v0.9.0 supports reading xml metadata from WarpTools to calculate the 3D-CTF: https://github.com/SBC-Utrecht/pytom-match-pick/releases/tag/0.9.0 

QFit 2025 improvements include reduced run time for ⁠qFit-ligand, the ability to use mmCIF files for both input and output, and an updated refinement pipeline that can place alternative location water molecules: https://github.com/ExcitedStates/qfit-3.0/releases/tag/2025.1

SAMtools 1.2.2 changes the default output CRAM version from 3.0 to 3.1. HTSlib no longer fetches CRAM reference data from EBI's server by default. A new command, samtools checksum, was added, as well as a variety of new options: https://github.com/samtools/samtools/releases

Scipion 3.7.1 was updated to include new tomography plugins for the CryoEM image processing framework including RelionTomo, AreTomo, Imod, Dynamo, MembrainSeg, DeepFinder, cryoCARE, Gapstop_TM, and EMReady 2.0, among others. Scipion's core was also updated to the latest versions: scipion-em-pyworkflow v3.11.1 and scipion-em v3.10.1, scipion-app 3.8.1: https://scipion-em.github.io/docs/release-3.0.0/docs/user/tutorials/tomo/tomography-intro.html 

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

Topaz 0.3.9  and 0.3.10 are now available: https://github.com/tbepler/topaz/releases/tag/v0.3.10

Vesicle-Picker 0.1.0-cs4.7 is compatible with cryosparc 4.7.

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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