SBGrid Newsletter: August 2024

Dear Consortium Members and Affiliates,

Our August update includes details about our new SBGrid publication, a first look at speakers for this season's software webinars, a software push with eight updated titles and five new tools, five new members to welcome, and two publication highlights.  

We're excited to announce a recently published manuscript describing the Capsules technology used to deploy SBGrid and BioGrids software collections. Read more in Acta Crstallogr D Struct Biol special 7tth ICUR, available via open access: https://doi.org/10.1107/S2059798324004881

Planning is underway for our 2024-2025 software webinar series and we will fill in  additional dates as speakers are confirmed. We welcome suggestions, so please email Michelle Ottaviano if there are any new or updated titles you would like to learn more about.

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

More dates coming soon!

Oct 8:  qFit - Stephanie Wankowicz, Ph.D 

Dec 10: AreTomo3 - Ariana Peck, Ph.D

May 13: DRGN-AI - Prof. Ellen Zhong

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, BUSTER, CCP4, CcpNmrAnalysis, cs2star, DENSS, PyMOL, and PyTOM, along with five new titles: AreTomo3, FoldTree, Molecular Nodes, PyTME, and relionsparc. See Software Changes below for complete details.

Five new members joined in the month of August: Daisuke Kihara of Purdue University, Melissa Davis from Morehouse School of Medicine, Marco DeVivo from Italian Institute of Technology, Edward Marcotte of University of Texas at Austin, and Elitza Tocheva from University of British Columbia. 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:

- Student contributor Vida Storm Robertson, now a PhD student at Caltech, highlighted a publication from SBGrid member Emina Stojković that appeared in Science Advances and shines new light on the machinery microbes use to observe the world,  revealing where photoelectric energy is converted into mechanical energy in a bacterial phytochrome and describing the formed, photoactive phytochrome structure. [Read more]

- Meharry Medical College student KeAndreya Morrison's highlight features a Nature Communications publication from the laboratory of SBGrid member Joshua Levitz and colleagues in which the authors examine how positive allosteric modulators (PAMs) improve the function and internalization of metabotropic glutamate receptors (mGluRs), potentially supporting the development of targeted neurological therapies. [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 five new citations since our last reporting, from these SBGrid members: 

Jennifer Bridwell-Rabb from University of Michigan in Biochemistry: Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein; Catherine Drennan of MIT in Biochemistry: How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase; Eric Fischer from Dana-Farber Cancer Institute in Nature Chemical Biology: Template-assisted covalent modification underlies activity of covalent molecular glues; Guilherme Martins Silva of Lijun Sun's lab at Beth Israel Deaconess Medical Center in International Journal of Biological Macromolecules: Structural analysis and shape-based identification of novel inhibitors targeting the Trypanosoma cruzi proteasome; Guillaume Poncet-Montange from the Broad Institute in Nature Cancer: BRD-810 is a highly selective MCL1 inhibitor with optimized in vivo clearance and robust efficacy in solid and hematological tumor models; Dirk Slotboom of University of Groningen in Nature Communications: Structural basis of the obligatory exchange mode of human neutral amino acid transporter ASCT2

AreTomo3 is new to SBGrid. AreTomo3 is a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.

autoPROC release 20240710 includes a new tool (aP_fit_wvl_to_spots) for analyzing processed datasets for a potential error in wavelength, improved handling of HDF5 datasets (via *_master.h5 files) when encountering different data types, and a number of fixes.

BUSTER release 20240710 adds a new tool (cif2tls) that will extract TLS information, along with a large number of improvements and fixes.

CCP4 version 9 brings various bugfixes and updates to multiple system components, including a new version of coot.

CcpNmrAnalysis 3.3.2 comes with extensive upgrades to the screening and metabolomics functions, including spectra simulation useful for working with metabolomics data and unknown substances.

cs2star 0.6.6 includes bug and compatibility fixes

DENSS version 1.7.3 include many bug fixes along with speed and stability improvements. Users can also utilizes a new script (denss.mrc2sas. py) that fits a calculated scattering profile from a density map to experimental SWAXS data and calculates chi2 as a metric of the quality of fit. Similar fits are also now produced using denss.py, denss.refine. py, and denss.all. py. 

FoldTree 20240730 is another new title in the SBGrid collection. FoldTree is a snakemake workflow for making and benchmarking structure based trees using Foldseek.

Molecular Nodes 4.2.4 is also new to SBGrid. Molecular Nodes is a tool that enables quick import and visualisation of structural biology data inside of Blender.

PyMOL 3.0.4 is a maintenance and bug fix release

PyTME 0.2.3, also new. PyTME is a software for data-intensive n-dimensional template matching on tomographic electron microscopy data using CPUs and GPUs. It includes a GUI that provides simplified mask creation, interactive filter exploration, result visualization, and manual refinement capabilities. It also offers specialized tools such as wedge masks, CTF correction, as well as means for handling structural data.

PyTOM 1.1 now includes a GUI and GPU support. The GUI includes a full pipeline and project management and GPU support includes reconstruction, template matching, real-space subtomogram alignment, and CPCA classification. Also new is the WarpM/RELION integration with xml-to-star conversion and IMOD integration with alignment import.

reliosparc bc3e5d6 is the last of the new software titles. relionsparc is a python based utility for converting cryosparc .cs files to a format suitable for Relion.

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