SBGrid Newsletter: April 2025

Dear Consortium Members and Affiliates,

April brought a moment of academic solidarity to brighten the spirit, and with that we continue onward, with a reminder about SBGrid laptop software installation options, an upcoming DRGN-AI webinar, a software push with 16 updates and 12 new titles, three new members to welcome, and two member publication highlights. 

SBGrid users can request personal credentials for our software installation manager to set up your home workstations with laptop and desktop-friendly titles for visualization or data processing workflows, which might include:

• visualization (Coot, ChimeraX, PyMOL)
• crystallography (CCP4, Global Phasing, Phenix, XDS, xds-gui)
• cryoEM (ChimeraX, Phenix)
• NMR (POKY, CCPN)

This tool provides a graphical interface, with push-button installation as well as CLI options, alerts users when software updates are available, and includes the latest news about new software added to the SBGrid collection and upcoming webinars. Request credentials here: https://sbgrid.org/registration/register/

We have two dates left in this season's software webinar series. First up is Ellen Zhong, who will give us a tour of DRGN-AI on May 20th. In case you missed our April webinar - A Hitchhiker’s Guide to Structural Cryo-ET in Warp 2.0 & Friends - with Alister Burt, you can watch the video on SBGridTV.

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

NEW DATE - May 20 : Ellen Zhong - CryoDRGN-AI: Neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets

June 10:  Genki Terashi - DiffModeler & CryoREAD: Macromolecular and Nucleic Acid Structure Modeling for Cryo-EM Maps Using Deep Learning

Sept & beyond: let us know what software tools you'd like to learn more about!   

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 Belmont University.

This month's software push includes updates to AlphaPulldown, AreTomo3, Chai-1, Fpocket, IDPConformerGenerator, IMOD, JupyterLab, pdb_extract, PEET, PROPKA, RDKit, RECOVAR, relion_composite_masks, Tardis, Warp, and XDS along with 12 new titles: AR-Decon, Cryo-MEM, HPN-SSH, MAVEn, MDCatch, Miffi, NMRFxAnalyst, NMRFxStructure, NuFold, SIREn, TomoCPT, and VISDEM. See Software Changes below for complete details.

Three new members joined in the month of April: Lindsey Backman from Whitehead Institute, Peter Dahlberg from Stanford University, and Justin Taraska from the NIH. 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 publication from SBGrid member Graeme Conn, of Emory University School of Medicine, who provides a compelling review of the antibiotic resistant causing protein MexXY. [Read more]

- Meharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a PNAS publication from the laboratory of Paul Riegelhaupt of Weill Cornell Medicine that reveals how anesthetics shut down brain activity by closing the THIK1 potassium channel, offering new insight into how anesthesia works at the molecular level. [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 six new citations since our last reporting, from these SBGrid members: 

Erin Adams and Anthony Kossiakoff from of University of Chicago in Nature Scientific Reports: Mapping the extracellular molecular architecture of the pAg-signaling complex with α-Butyrophilin antibodies; Sébastien Granier from Institut de Génomique Fonctionnelle in Nature Communications: Inactive structures of the vasopressin V2 receptor reveal distinct binding modes for Tolvaptan and Mambaquaretin toxin; Sun Hur from Boston Children's Hospital and HHMI in Molecular Cell: Ultrastable and versatile multimeric ensembles of FoxP3 on microsatellites; Daniel Hurdiss and Frank Van Kuppeveld from Utrecht University in Nature: A coronavirus assembly inhibitor that targets the viral membrane protein; Maria Spies and Nicholas Schnicker from University of Iowa Carver College of Medicine in Nature: The RAD52 double-ring remodels replication forks restricting fork reversal; and Edward Twomey from Johns Hopkins University School of Medicine in Nature: Glutamate gating of AMPA-subtype iGluRs at physiological temperatures.

AR-Decon 551fc84 is a CryoEM post processing tool that enhances the quality of three-dimensional maps that suffer from anisotropic resolutions, often resulting from datasets with preferred orientations. By applying advanced deconvolution techniques, AR-Decon corrects these resolution discrepancies, leading to more accurate and isotropic 3D maps. Learn more: https://github.com/yifancheng-ucsf/AR-Decon

Cryo-MEM 3dff057 is a software for membrane signal subtraction to facilitate high-resolution cryo-EM reconstruction of membrane proteins embedded in their native membrane environment. Learn more: https://github.com/JackZhang-Lab/Cryo-MEM/blob/main/Mem_subtraction/doc/en/Workflow_en.md.

HPN-SSH 18.6.2 is a high performance fork of OpenSSH that can provide significantly faster throughput for bulk data transfers over a wide range of network paths. Learn more: https://github.com/rapier1/hpn-ssh.

MAVEn 1.0 is a tool for the systematic analysis of compositionally-heterogeneous cryo-EM datasets. MAVEn is designed to work downstream of cryoDRGN, after users have generated a large number of maps (usually 500-1000) systematically sampling the latent space, but can be applied to any ensemble of volumes. Learn more: https://github.com/lkinman/MAVEn.

MDCatch 2.5 fetches acquisition metadata from an EPU session or SerialEM, parsing the first found xml/mdoc/mrc/tif file (from EPU/SerialEM) associated with a data collection session and launching Relion 4 or Scipion 3 pipelines. Learn more: https://github.com/azazellochg/MDCatch

Miffi 1.0.0 offers improved accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information. Learn more: https://github.com/ando-lab/miffi?tab=readme-ov-file

NMRFxAnalyst 11.4.20 is a software application for processing, visualizing, and analyzing NMR datasets, enabling researchers to convert raw data into spectra for downstream analysis, including peak-picking, assignment, and structure calculation. It supports a variety of NMR data types and provides tools for analyzing small molecules, proteins, RNA, DNA, and metabonomics datasets. Learn more: https://nmrfx.org/nmrfx/analyst

NMRFxStructure 11.4.20 is a software tool for generating and analyzing macromolecular structures and predicting chemical shifts, offering both predefined modes and customizable scripting via Jython. It supports structural analysis and prediction, enhancing research in structural biology and NMR spectroscopy. Learn more: https://nmrfx.org/nmrfx/structure.

NuFold 1.0 is a state-of-the-art method designed for predicting 3D RNA structures, leveraging deep learning for high accuracy and reliability. This tool is particularly useful for biologists and bioinformatics researchers focusing on RNA function and structure. Learn more: https://github.com/kiharalab/NuFold

SIREn 1.0.0 is a toolkit for analyzing heterogeneity in 3D volume ensembles generated via cryo-EM. SIREn performs automated detection of structural blocks to allow model-free detection of heterogeneity and includes a 3D Convolutional Neural Network (CNN) to predict binarization thresholds for 3D density maps. Learn more: https://github.com/lkinman/SIREn 

TomoCPT 23f0a2b (tomogram Centroid Prediction Tool) is a deep learning based program for enabling centroid prediction of objects in 3D cryo-tomograms. Learn more: https://github.com/shahpnmlab/tomocpt

VISDEM 1.2 is a cryo‑EM density map sharpening tool that estimates the underlying atomic distribution of a protein from the density map and computes the corresponding radially averaged structure factor and density histogram. Learn more: https://github.com/gschroe/visdem

AlphaPulldown was updated to release 2.0.3. Since our last update, this version includes workflow automation, critical bug fixes for sequence pairing functionality affecting prediction accuracy since August 2023. Other improvements include unified configuration syntax across all AlphaPulldown modes, support for multiple modeling backends including UniFold, AlphaLink2, and experimental AlphaFold3, cross-link-driven modeling with XL-MS data integration, significant storage optimization using compression techniques, and ModelCIF format support for improved accessibility

Release notes: https://github.com/KosinskiLab/AlphaPulldown/releases

AreTomo3 release 2.1.3 is now available.

Chai-1 0.6.1 adds significant template support, MSA subsampling capabilities, and multiple dependency improvements while fixing several template-related bugs.

Fpocket 4.2.1 adds an M1/M2 chip mofile plugin and fixes a pdbx plugin bug from vms for read spurious atom_site elements.

IDPConformerGenerator 0.7.25 adds a method for generating all-atom conformations of intrinsically disordered regions (IDRs) at N- and C-termini of and in loops or linkers between folded regions of an existing protein structure. Release notes: https://idpconformergenerator.readthedocs.io/en/latest/. 

IMOD 5.2.1b includes new features and improvements to the electron microscopy tomography software suite, building upon the stable 5.1 release.

JupyterLab 4.4.0 includes a new Settings Import feature from a JSON File and support for kernel subshells along with a number of improvements and several bug fixes. Release notes: https://github.com/jupyterlab/jupyterlab/release.

PEET 1.18.0 includes an update to Matlab R2023b, support for maca64 systems in native mode, and the addition of polarPlot and renumberParticles.

pdb_extract 4.3 improves metadata handling, checks output for deposition readiness, and enables template downloads for related structures, including map-only options for 3DEM, alongside improved log parsing.

PROPKA 3.5.1 is an update to the codebase with Python 3.8-3.11 support, improved type safety, fixes to a number of calculation bugs, and enhanced ligand atom handling that includes a fix to precision issues in pI calculations and folding profile reporting, corrected vanadium symbol from Va to V, increased valence electrons for ligand atoms, and a fix to a conformational analysis bug in "topping up" process. 

RDKit 2025.03.1 adds experimental synthon-based substructure and similarity search capabilities for large combinatorial spaces, along with significant performance improvements in CIP labeling, Morgan fingerprints, and conformer generation, plus numerous bug fixes and API enhancements. Release notes: https://github.com/rdkit/rdkit/releases

RECOVAR 0.4.4 provides a different user interface.

relion_composite_masks 20250314_cu12.2 is a new build based on Relion 5.0. It includes all of the features of Relion 5 in addition to composite masks. Versions for CUDA 11.3 and 12.2 are now available. 

Tardis 0.3.10 adds napari support, fixes in model versioning, and updates all models. Release notes: https://github.com/SMLC-NYSBC/TARDIS/releases

Warp 2.0.0dev33 version is the latest minor developer release and includes minor bug fixes.

XDS 20250327 includes error corrections and improvements in background estimation, particularly enhancing the calculation of correction tables, handling of diffuse scattering, and refinement of profile fitting routines.

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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More information about the SBGrid Consortium is available at https://sbgrid.org

Report software bugs: sbgrid.org/bugs