SBGrid Newsletter: October 2023

Dear Consortium Members and Affiliates,

The SBGrid Halloween update includes a reminder to register for our webinar series including our November DiffDock webinar, a software push with 18 updates and two new titles, six new members to welcome, and two member publication highlights.

We kicked off our software webinar series in October with a presentation from Pablo Conesa on ScipionTomo. If you missed this webinar you can find the recording on SBGridTV. Next up we'll learn more about the DiffDock method for molecular docking from Gabriele Corso, Hannes Staerk, and Bowen Jing.  [Register here].

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: 

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 ATSAS, BCFtools, Bowtie 2, crYOLO, deepTools, Fiji, HHsuite, IGV, ilastik,  ImageJ, IMOD, Model-Angelo, pdb-tools, ProDy, PyEM, SAMtools, XDSCC12, and XDSSTAT, along with two new titles:  IPA and Uni-Dock. 

See Software Changes below for complete details.

Six new members joined SBGrid in October: Amanda Chaplin of University of Leicester, Ariane Mbemi Chitoh from Jackson State University, Sladjana Prisic from University of Hawaii at Manoa, David Sherman from University of Michigan, Wei-Jen Tang from University of Chicago, and Arbor Biotech. 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 Tamir Gonen of University of California, Los Angeles that appeared in Advanced Science, in which the authors describe their use of MicroED to determine the conformational states of the commonly prescribed medication Mirabegron. [Read more]

- Meharry Medical College student KeAndreya Morrison's October highlight appeared in SLAS Discovery from Karolin Luger of University of Colorado, Boulder and colleagues, this publication describes the development of a new high throughput assay screening for PARP1-HPF1 complex inhibitors that may open doors for discovery of new cancer therapeutics. [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 three new citations since our last reporting, from these SBGrid members: Karolin Luger of University of Colorado, Boulder in Nature Microbiology: Histones with an unconventional DNA-binding mode in vitro are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus; SBGrid members Eric Girard and Dominique Madern from Université Grenoble Alpes in Molecular Biology and Evolution: Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery, and Jean-Philippe Julien from The Hospital For Sick Kids/University of Toronto in Cell Reports: Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein.

ATSAS 3.2.1 is now available.

BCFtools 1.18 includes support for auto indexing during writing BCF and VCF.gz via a new --write-index option along with changes to many commands. See the release notes.

Bowtie 2 2.5.2 fixed issues preventing bowtie2 from utilizing the specified number of CPU cores, causing bowtie2 to segfault when reading compressed inputs on Windows, an issue causing bowtie2 to segfault while parsing interleaved reads, and overhauled the FASTQ parser with better tolerance for empty lines.

CrYOLO 1.9.6 fixed the reading method for eman filament start-end files.

deepTools 3.5.4 is available. See the release notes for full details.

Fiji 2.14 is now available.

HHsuite 3.3.0 includes a -premerge option to improve contact prediction performance and adds SIMDe library support for ARM, PowerPC, and all kinds of SIMD standards.

IGV 2.16.2 fixed a problem loading BAM files from 10X Genomics that contain out-of-spec MM tags.

ilastik 1.4 is the latest stable release and the new default. This version includes major user interface updates and performance improvements for the Multicut Workflow, stability and usability improvements to the Carving Workflow, new redo/undo options for brush-strokes, and a new Neural Network Workflow to run pre-trained neural networks from Bioimage.io Model Zoo on CPU, GPU, or on a remote server.

We also pushed out the ilastik beta version 1.4.1b7, which adds a new Trainable Domain Adaptation Workflow, Tiff reading improvements, and improvements to the mMulticut user interface.

ImageJ  is now at release 1.53t.  

IMOD was updated to the latest nightly release - 4.12.52 - which is available via version override.

IPA is new to SBGrid at version 1.0. IPA or Iterative Projection Algorithms for protein crystallography is used for ab initio phase determination.

Model-Angelo 1.0.5 fixes an issue with esm model loading.

pdb-tools version 2.5.0 is the new default.

ProDy 2.4.1 is the new default.

PyEM was updated to 20231010

SAMtools 1.18 includes improvements to minimiser sort options, a new --duplicate-count option that adds the number of duplicates to the original read in a dc tag, a calmd update to handle unaligned data or empty files, more consistent flag filtering for fasta/fastq with --rf/ --incl[ude]-flags and long options for -F (--excl[ude]-flags and -f (--require-flags), an option to specify length using import --order TAG to --order TAG: length, and new --aa mode for consensus.

Uni-Dock is new to SBGrid at version 1.0.0. Uni-Dock is a GPU-accelerated molecular docking program developed by DP Technology. It supports various scoring functions including vina, vinardo, and ad4. 

XDSCC12 2020-12-9 is now available

XDSSTAT was updated to release 12.5.2023

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

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