SBGrid Consortium - News and Events

Newsletter for May 2021

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Published May 2021

Dear Consortium Members and Affiliates,

As we head into a holiday weekend here in the States, we're feeling relieved to have warmer weather, an extra day away from the screen, and vaccination numbers continuing to rise. The SBGrid team is preparing for July renewals, and has done a bit of reconfiguring to introduce add-on software options. We have two June webinars for your calendar (with May webinars now available on YouTube), 9 software updates, 2 new titles, 3 member publication highlights and 3 new SBGrid citations.

A final reminder to please contact us if you would like to opt-in to include any of the fee-based add-on software options in your SBGrid renewal. Invoices will go out in June for July renewals and non-profit users will need to opt-in to access the following software:

•	BioGrids: a collection of ~400 bioinformatics software titles accessible in an SBGrid-style format. (Note: this option does not replace the existing bioinformatics titles included in SBGrid, but is a more comprehensive collection available to labs involved in more computational work).

•	The Schrodinger Drug Discovery platform (license limited to labs in North America and Australia).

•	Geneious, a leading bioinformatics software platform.

Many groups expressed an interest in accessing pre-configured CryoEM workstations, and we'll have more information soon about opportunities to participate in a pilot program.

This month's software push includes 9 updates - AmberTools, BioXTAS RAW, cryoDRGN, crYOLO, ISOLDE, DeepEMhancer, Ffmpeg, IMP, and TomoAlign - and two new titles: AutoDock-GPU and novaCTF. See Software Changes below for complete details.

May also brought 3 new members: Roshan Paudel from Morgan State University, Philip Kranzusch from Dana-Farber Cnacer Institute, and Mark Namchuk from Harvard Medical School. Welcome to our newest members!

We're wrapping up our webinar series for the season, with two final software talks in June. Check the SBGrid YouTube channel for recordings of our May webinars with presentation on on KLTPicker, EMAN2, and LightDock.

We're already starting to fill in dates for September, so if you've got a story to tell or would like to hear more about a particular software title, contact Michelle at ottaviano@hkl.hms.harvard.edu.

Upcoming SBGrid Weekly Webinars

June 8 - Dynamo - Daniel Castaño Díez

June 29 - HADDOCK - Alexandre Bonvin

July & August - summer break

Sept 14 - MoRDa - Andrey Lebedev

Webinar details here

Member Publications

Over 90 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 new Nature paper from Hao Wu of Boston Children’s Hospital and Jianbin Ruan of the University of Connecticut Health Center details their cryo-EM structure determination of the gasdermin D pore and prepore, a protein instrumental in driving pyroptosis. They describe how the GSDMD pore mediates IL-1 release by electrostatic filtering, which suggests that charge may play an important factor in pore transport. [Abstract]

•

In a new publication in PLoS Pathogens, Chi-Min (Mimi) Ho of Columbia University reviews transport activities at the vacuolar compartment created during the malaria parasites' invasion of host cells, crucial to parasite survival and propagation. The review focuses on recent advances in the research on effector protein translocation into the host cell by PTEX and small molecule transport by EXP2. [Abstract]

•

From our graduate student desk, Harvard student Kristen Rodrigues highlighted a publication in Cell Reports from the laboratory of James Crowe of Vanderbilt University describing their investigation of antibodies against New World hantaviruses, a group of viruses that cause cardiopulmonary syndrome with a high fatality rate. [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 3 new citations in the month of May, from these SBGrid-member laboratories: Catherine Drennan from MIT in ACS Omega:

Crystal Structure of the [4Fe–4S] Cluster-Containing Adenosine-5′-phosphosulfate Reductase from Mycobacterium tuberculosis; Frank Sicheri from University of Toronto in Structure: Bipartite binding of the N terminus of Skp2 to cyclin A; and a publication in Neurology with contributions from SBGrid members Jens Meiler of Vanderbilt University and Jonathan Sheehan of Washington University in St. Louis: Familial Autonomic Ganglionopathy Caused by Rare CHRNA3 Genetic Variants

Software Changes

AmberTools version 21 includes new and updated forcefields, ReaxFF for reactive molecular dynamics that supports a wide variety of chemical behavior, new ion parameters for the OPC, OPC3 water models and for some modified amino acids, quick package for Hartree-Fock and DFT electronic structure calculations, with GPU support. Quick is integrated into sander for QM/MM simulations. AmberTools is also now compatible with gcc10/gfortran10.

AutoDock-GPU 1.3 is new to the SBGrid collection. This Cuda-accelerated version of AutoDock4.2.6, leverages what developers call its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units.

BioXTAS RAW 2.1.0 is the new default and includes some major changes. Users can now save data analysis reports as PDFs and will notice a GUI for the REGALS technique, a new way to deconvolve overlapping LC-SAXS peaks. The developers also overhauled the auto_guinier function to improve accuracy and applicability to lower quality data, added a new, more accurate method for automatically finding Dmax when using GNOM, and pushed out several bug fixes and minor improvements. Note for MacOS users: The prebuilt version of RAW will now run only on 10.11 or later.

cryoDRGN 0.3.2 has a new command - cryoDRGN_filtering.ipynb - for interactive filtering/selection of images from the dataset and a new cryodrgn view_config option along with minor performance improvements and compatibility fixes.

crYOLO beta version 1.8.0b28 is now available via version override, with new options for a tomography picking mode that works with single particles and filaments and increased filament support (crYOLO now learns end-to-end to estimate the filament direction). Note, however, that you will need to retrain your models to use this feature with old filament models. For filaments, crYOLO creates two additional folders: CBOX, containing the crYOLO picked particles that are input for filament tracing, and CBOX_FILAMENT_SEGMENTED, which contains segmented filaments in CBOX format and allows live filtering via the confidence threshold in the BoxManager. Also new is an option for full random rotation, several library updates as part of the transition to tensorflow2, options to use .star files as input during prediction, and an update to 1.4.0 for BoxManager.

DeepEMhancer 20210511 is a cuda11 version and is available via version override. Note that the standard models distributed via DeepEMhancer will not work with this version and corrected models are distributed alongside in /programs/share/deepemhancer.

FFmpeg is now at release 4.44.4. Version 4 is a new major release.

IMP was bumped to 2.14.0.

ISOLDE 1.2 (check Tristan Croll's Twitter feed for more details) offers the ability to extend protein chains (first select an existing terminal residue, then "isolde add aa {resname} sel" to add a new one), also new "quick" and "medium" simulation fidelity modes for ~4X performance improvements on lower-end GPUs, new commands "isolde write phenixRefineInput" and "isolde write phenixRsrInput" to write input files with recommended settings for refining ISOLDE-rebuilt models, significant improvements to stability and performance of bulk solvent/scaling in crystallographic datasets, and for the power user, an "isolde shorthand" command that creates a series of 2-4 character aliases for commonly-used commands and prints a handy cheat-sheet to the log that users can enable permanently with the addition of "isolde shorthand" to the Startup tab under Favorites/Settings.

novaCTF is new to SBGrid at version 20181108. NovaCTF provides 3D-CTF correction for cryo-electron tomography.

TomoAlign was updated to version 202103, which includes significant changes, updated documentation, and a new tutorial.

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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