SBGrid Consortium - News and Events

Newsletter for May 2023

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Published May 2023

Dear Consortium Members and Affiliates,

It's time for our May recap of news from the SBGrid team, including a reminder about annual SBGrid renewals, a farewell and a welcome to our student contributors, links to catch up on the latest SBGrid webinars and register for the June 13th presentation on POKY, a software push with ten updates and five new titles, three new members to welcome, a solution to the MacOS Ventura code-signing issues, and three member publication highlights.

The SBGrid annual renewal season is upon us, with a common anniversary date of July 1. We're happy to report that despite rising costs on many fronts, the rates for access to the SBGrid software collection will not increase. A quirk of the Harvard system is that we are not allowed to collect renewal payments until July 1. We'll be in touch soon with renewal invoices, but rest assured that SBGrid support will continue uninterrupted during the month of July as payments are being processed. Please let us know of any membership changes for the coming year or if you would like to change your elections for the BioGrids, Geneious, and Schrodinger add-on options (see availability restrictions for each below):

•	BioGrids: an SBGrid-style collection of 500+ bioinformatics applications. Cost: $600 per lab for non-profit groups. Industry users, please contact us if you are interested in a quote to add BioGrids to your site.
•	Geneious (available to non-profit labs): shared license for this bioinformatics software platform. Cost: $425 per lab. Note: we have increased the number of shared licenses and implemented some changes to optimize license server performance.
•	Schrödinger (available to non-profit labs in North America and Australia): 125 floating tokens supporting visualization/testing/small jobs. Cost: $1,000 per lab.

If you've been reading our newsletters for a while, you may have noticed contributions from Harvard/MIT student Kristen Rodrigues to our SBGrid member publication highlights each month since 2016. She has now completed her PhD (congrats Kristen!) and is on to bigger things, but is graciously passing the baton to our new student correspondent: Vida Storm Robertson from Fisk University. Check our Publication Highlights section for Kristen's final report and the first from Storm!

June 13th is the last SBGrid webinar of the season, when Prof. Woonghee Lee will join us to present POKY, a software suite for multidimensional NMR spectroscopy and three-dimensional structure calculation of biomolecules. In the meantime, check the SBGrid YouTube channel for the latest presentations from Kevin Dalton on careless and Gustaf Ahdritz on OpenFold.

Upcoming SBGrid Webinars

June 13th - Prof. Woonghee Lee, POKY

Sept 2023: our new season begins. Let us know if you would like to hear more about a particular software title!

Webinar registration and details here

For our May software push we have updates to AlphaPulldown, bedtools, CellProfiler, ChimeraX, cryoDRGN, Model-Angelo, PyMOL, Schrödinger, SRA Toolkit, TomoTwin-cryoET, and five new tools for the SBGrid collection: DataWarrior, mcm-cryoet, MDtraj, PyEMMA, and PyHI. See Software Changes below for complete details.

We had three new members join in the month of May: Kliment Verba of University of California, San Francisco, Matthias Haury from Chan Zuckerberg Institute for Advanced Biological Imaging, and Wade Harper from Harvard Medical School. Welcome to our newest members!

Technical notes from our Software Team

We've developed a solution to make the MacOS Ventura workaround (https://sbgrid.org//wiki/macos) for code-signing issues unnecessary and are currently working our way through the collection. If you see a "this application is damaged" message, please let us know at bugs@sbgrid.org and we'll prioritize a fix for that application.

Member Publications Highlights

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.

•	A primer in PLoS Biology from Jianbin Ruan of the University of Connecticut Health Center discusses pyroptosis, its mediation by pore-forming proteins called gasdermins, and the evolution of the gasdermin family across metazoans. [Abstract]

•

From our out-going graduate student desk, Harvard student Kristen Rodrigues highlighted a publication from the laboratory of Aaron Whiteley at the University of Colorado, Boulder that appeared in Cell in which the authors demonstrate that bacteria express anti-phage proteins containing a NACHT module, which is an important element of the animal nucleotide-binding domain leucine-rich repeat containing gene family called NLR. [Read more].

•

From our incoming graduate student desk, Fisk University student Vida Storm Robertson highlighted a Journal of Pharmacology and Experimental Therapeutics publication from Tao Che's laboratory at Washington University in St. Louis. Using cryo-EM, the authors studied the specificity of the κ-opioid receptor to ligands and the selectivity of four types of Gi/o-family proteins to the KOR/ligand complexes. [Read more].

Deposit your experimental datasets: 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.

Acknowledge SBGrid: 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 citations: SBGrid's eLife paper received four new citations in the month of May, from these SBGrid-member laboratories:

Jean-Philippe Julien of Hospital for Sick Children Research in Science Translational Medicine: A multi-specific, multi-affinity antibody platform neutralizes sarbecoviruses and confers protection against SARS-CoV-2 in vivo; Tina Iverson with Terunaga Nakagawa at Vanderbilt University in PLOS ONE; CryoEM structure of a post-assembly MS-ring reveals plasticity in stoichiometry and conformation; Jeremy Nathans with Sandra Gabelli of Johns Hopkins University School of Medicine, in PNAS: Structure of WNT inhibitor adenomatosis polyposis coli down-regulated 1 (APCDD1), a cell-surface lipid-binding protein; and Dhirendra K. Simanshu of the Frederick National Laboratory for Cancer Research in a contribution to the Journal of Biological Chemistry: The Ribosomal S6 Kinase 2 (RSK2)-SPRED2 complex regulates phosphorylation of RSK substrates and MAPK signaling.

Software Changes

AlphaPulldown 0.30.5 includes a fix to set the pdbfixer version to 1.6.0 when creating the conda environment and fixes the error of ``template_confidence_scores```.

bedtools 2.31.0 includes a new summary tool for basic sanity checks and quality control of interval files and support for gzipp'ed FASTA files to getfasta and nuc, along with a few minor bug fixes.

CellProfiler 4.2.5 fixes 3D object loading and subsample values >1 overwriting input image, adds a patch for headless creation of properties files, and updates resize.py.

ChimeraX 1.6 is out. This version includes ESMFold protein structure prediction and residue-residue error plot and new GUIs for Add Charge, Dock Prep (to repair side chains, add hydrogens, etc), and for rendering by Attribute for coloring by atomic or residue values. Also new is a swapna command to mutate nucleic acid residues and options to invert chiral center, read SwissDock docking results, paste in a Blast Protein query sequence or specify it by UniProt ID, browse/fetch medical images from The Cancer Imaging Archive, and read medical images in NIfTI (.nii) and NRRD (.nnrd) formats.

cryoDRGN 2.3.0 updates the model configuration files to save as human-readable config.yaml files, fixes the machine stamp in output .mrc files for better compatibility with downstream tools, adds better documentation of help flags in ab initio reconstruction tools, and updates functionality in cryodrgn_utils filter_star.

DataWarrior 5.5.0 is one of five new tools added this month. DataWarrior is a program for interactive data analysis and visualization of particular interest for cheminformaticians because chemical structures and reactions are native datatypes and because of its rich cheminformatics functionality.

mcm-cryoet aee4593 is new to SBGrid. Mean curvature motion and levelset motion for cryo-ET (mcm-cryoet) is a method applied to segmentation results to significantly improve both the visual quality and downstream computational handling based on nonlinear anisotropic diffusion.

MDtraj 1.9.7 is also new tool in the SBGrid collection. MDtraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories with wide MD format support (including pdb, xtc, trr, dcd, binpos, netcdf, mdcrd, prmtop, and more), fast RMSD calculations, and extensive analysis functions including those that compute bonds, angles, dihedrals, hydrogen bonds, secondary structure, and NMR observables.

Model-Angelo is now at version 1.0.1 and with the 1.0 release there is added support for nucleotides and protein identification and a new option to access HMM search utilities straight from ModelAngelo output folders.

PyEMMA 2.5.12 is another new addition. PyEMMA - Emma’s Markov Model Algorithm is a Python library for the estimation, validation and analysis of Markov models of molecular kinetics and other kinetic and thermodynamic models using molecular dynamics data.

PyHI 8a98c25 is the last of the new titles. PyHI is a Python-based graphical interface for indexing power spectra of helical assemblies.

PyMOL 2.5.5 includes fixes for set_name error, crashing when loading a discrete object, TypeError for Lighting Plugin, a problem using Build Residues from the menu.

Schrödinger version 2023-2 is now available. Note: the SBGrid Schrödinger license is only available to non-profit labs in North America and Australia who opt-in for this add-on tool.

SRA Toolkit is at version 3.0.5, which includes added support for PacBio to fasterq-dump, a new option to output reference sequences to fasterq-dump, and a bug fix in dbGaP data access when using ngc files.

TomoTwin-cryoET 0.4.0 is the official clustering workflow release along with a in-depth turtorial. You also may notice new tools like tomotwin_tools umap and tomotwin_tools embeddings_mask.

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.

This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium, the Structural Biology Grid computing consortium.

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

Report software bugs: sbgrid.org/bugs

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