SBGrid Newsletter: November 2023

Dear Consortium Members and Affiliates,

November news from the SBGrid team includes a profile on SBGrid member Sarah Bowman, software webinars updates with an upcoming presentation on DeepFoldRNA and a recording of the DiffDock webinar hosted earlier this month, a software push with 10 updates and three new titles, and two member publication highlights, 

The month's member tale features Sarah Bowman, who moved through her first undergraduate degree to a Denver bookstore, eschewing science all the way, until a chemistry class with a dynamic professor helped to put her on the path to structural biology. Bowman now leads her own lab at Hauptman-Woodward Medical Research Institute studying metalloproteins, heads up the National High-Throughput Crystallization (HTX) Center, and does community outreach to encourage others to enter the world of science. [Read more] 

Our November software webinar introducing DiffDock is now available on SBGrid's YouTube channel. Tune in on December 12th to learn more about DeepFoldRNA from Robin Pearce of Yang Zhang's lab at University of Michigan Medical School. Register here for the series.

Oct 10: ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation - Pablo Conesa
Nov 14: DiffDock - Gabriele Corso, Hannes Staerk, and Bowen Jing

Dec 12: DeepFoldRNA - Robin Pearce

Jan 9: DIALS - Graeme Winter

Feb 13: OccuPy  - Björn Forsberg
Mar 12: Relion5 - Sjors Scheres

Apr 9: RFdiffusion - Brian Trippe

May 14: Free energy methods in Amber - Darrin York

Jun 11: TomoDRGN - Joseph Davis

Webinar registration and details

This month's software push includes updates to AlphaPickle, AreTomo2, Careless, EMReady, Gnuplot, Julia, ModelAngelo, MotionCor3, Relion, and TomoTwincryoet, along with 3 new titles:  AutoGrow, GCtfFind, and Reinvent. See Software Changes below for complete details.

Seven new members joined in November: William Booth II of Winston-Salem State University, Steve Bonilla of Rockefeller University, Hua Deng of Morgan State University, Manuela Hospenthal from ETH Zurich, Toshio Moriya from High Energy Accelerator Research Organization (KEK), Emina Stojkovic from Northeastern Illinois University, and Harel Weinstein from Weill Cornell Medical College. 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:

- Fisk University student Vida Storm Robertson highlighted a publication from SBGrid member Chad Rienstra of University of Wisconsin-Madison and collaborators at University of Illinois at Urbana-Champaign who used solid-state NMR and rational drug-design to study amphotericin B selectivity for membrane sterols. [Read more]

- Meharry Medical College student KeAndreya Morrison's November highlight features a publication from SBGrid member Uhn-Soo Cho of University of Michigan Medical School and colleagues from the University of Southern California that appeared in Nature in which the authors investigate the non-canonical functions of the histone methyltransferase MLL1 and uncover a new role for centromere regulation by methylation of Borealin, one of the chromosome passenger complex proteins. [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 7 new citations since our last reporting, from these SBGrid members: 

Alexandra. Deaconescu of Brown University in Journal of Biological Chemistry: Structure of Phosphorylated-like RssB, the Adaptor Delivering σs to the ClpXP Proteolytic Machinery, Reveals an Interface Switch for Activation; Woonghee Lee, developer of POKY and NMRFAM-Sparky at University of Colorado, Denver in Journal of Magnetic Resonance: REDEN: Interactive Multi-Fitting Decomposition-based NMR Peak Picking Assistant; Jason McLellan from University of Texas at Austin in a collaboration with researchers at University of Cologne and others in Immunity: Single-cell analysis of memory B cells from top neutralizers reveals multiple sites of vulnerability within HCMV Trimer and Pentamer; John Pascal from Université de Montréal in Nucleic Acids Research: Structural and biochemical analysis of the PARP1-homology region of PARP4/vault PARP; Hao Wu from Boston Children's Hospital in Nature: Structural insights into cytokine cleavage by inflammatory caspase-4; Scientists at EMBL Grenoble in the European Journal of Medicinal Chemistry: Discovery of potent chromone-based autotaxin inhibitors inspired by cannabinoids; Scientists at IBS Grenoble in Journal of Virology: 

Toward the understanding of DSG2 and CD46 interaction with HAdV-11 fiber, a super-complex analysis  

AlphaPickle 1.5.4  fixes a bug  in the handling of command line arguments.

AreTomo2 1.0 is an open source implementation of AreTomo from the Chan Zuckerberg Imaging Institute.  

AutoGrow4 is new to SBGrid at version 4.0.3. AutoGrow4 is an evolutionary algorithm that optimizes candidate ligands for predicted binding affinity and other drug-like properties from the Durrant Lab at the University of Pittsburgh.

Careless is now at release 0.3.9. Since the ump to 0.3 Careless was updated to include a new command line script careless.xds2mtz to generate  mtz files for use with careless from XDS .HKL files. There are two new versions for mac:  0.3.9 and 0.3.9_arm, built for M1/M2 Silicon macs with macOS 12 or greater.

EMReady 1.1 includes performance improvements and memory optimization.

GCtfFind is new to SBGrid from the Chan Zuckerberg Imaging Institute. GCTFFind is a newly developed application for the CTF estimation of cryoET tilt series and cryoEM micrographs. The authors note that this release is an initial effort and feedback is greatly appreciated.

Gnuplot 5.4.9 includes support for building with Qt6, an update to check the plugin version at the time of import, and several other fixes

Julia was updated to 1.9.3

ModelAngelo 1.0.6 is the new default. This release includes much better HMMSearch, including all_hits.csv and best_hits.csv.

Motioncor3 is an open source implementation of MotionCor2, with the addition of CTF (Contrast Transfer Function) estimation in this multi-GPU accelerated software package that enables single-pixel level correction of anisotropic beam induced sample motion for cryo-electron microscopy and cryo-electron tomography images. From the Chan Zuckerberg Imaging Institute.  

REINVENT 4 is new to SBGrid. REINVENT is a molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design, molecule optimization, and other small molecule design tasks.

Relion 5.0-beta is now available via version override. New features include Blush regularization, which incorporates more prior knowledge into the cryo-EM refinement process useing a denoising convolutional neural network inside the iterative refinement algorithm of Class3D, Refine3D or MultiBody jobs. a new method called DynaMight that explores protein Dyna-mics, and Might improve your map’ for modelling continuous structural heterogenecity, a new utility to select subsets of filament particles that belong to the same structural class, support for GPU acceleration of relion-5 in HIP/ROCm and SYCL that results in more efficiency when running  relion_refine on AMD and Intel GPUs, and a new pipeline for sub-tomogram averaging (relion --tomo)  that starts with serialEM mdoc files and raw movies, and potentially ends with automated model building by ModelAngelo.

TomoTwin-cryoet 0.6.1 includes several performance improvements and bug fixes.

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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