SBGrid Consortium - News and Events

Newsletter for January 2021

Older
Newer

Published January 2021

Dear Consortium Members and Affiliates,

We're here, in a new year, that took until mid-month to feel real. Along the way we've accumulated the usual bits of SBGrid news to share, with a profile on SBGrid member Ernesto Fuentes from University of Iowa, the latest roster of webinars available online or coming soon, nine new members to welcome, a shiny new version of our sbgrid-cli software installation manager, a software update with 8 updates and one new title, and 4 member publication highlights.

Our January SBGrid Tale features Ernesto Fuentes, whose laboratory at University of Iowa College of Medicine spends much of its time teasing out the subtleties in PDZ domain interactions. Fuentes emphasizes the importance of using all the tools in the structural biology toolbox to dig deeper into the biology at work. [Read the full story].

We squeezed in a couple of webinars, this first month of the new year, with primers on emClarity from Benjamin Himes and DeepEMhancer from Rubén Sánchez Garcia. Check out these new recordings and a collection of over 100 other webinars on SBGrid's YouTube channel. We've got speakers lined up through March, but are always looking for suggestions, so if you have work you'd like to share or a software title you would like to hear more about, let us know!

Upcoming SBGrid Weekly Webinars

Feb 2 - Fabian Schoenfeld - GPU ISAC

Feb 9 - Jason Key - New CLI version - SBGrid Installation Manager

Feb 16 - Paul Emsley - Coot

Feb 23 - Yilai Li - CryoAssess

Full schedule and connection details here

We had a small software push this month with updates to CCP4, CCPNMR, cryoDRGN, DIALS, IMOD, PEET, Phenix, and sbgrid-cli, and 1 new title: LightDock. See Software Changes below for complete details.

The new year brought us nine new members, including Isabelle Rouiller at University of Melbourne, Kevin Campbell at University of Iowa, Edward Twomey from Johns Hopkins University School of Medicine, along with 6 new members at Westlake University in China: Huaizong Shen, Jing Huang, Dan Ma, Qi Hu, Hongtao Yu, Jianping Wu. Welcome to our newest members!

Technical notes from our Software Team

We have updated our command-line installation manager, "sbgrid-cli", to version 2.1.3 (2.1.4 is coming soon). This new version, available for Mac and Linux, has many improvements including multithreaded rsync transfer, selectable installation target path, and network diagnostics for troubleshooting.

For those who are using an old version, there is no need to re-register or reactivate, you can just download the latest from our wiki at https://sbgrid.org//wiki/sbgrid-cli.

If you haven't yet tried sbgrid-cli installation manager, you can register for access at www.sbgrid.org/registration/register/, then see the wiki for installation details.

Member Publications

Over 50 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:

•	In PLoS Computational Biology, a new paper from Jens Meiler of Vanderbilt and Leipzig Universities delves into the wonderful world of Rosetta and novel computational protein design with the debut of ResCue (residue-coupling enhanced). This method addresses the shortcomings of current protocols that neglect to harness co-evolutionary information in protein function to guide protein design. [Abstract]
•	The University of California, Berkeley's James Hurley and Marc Allaire present the solved crystal structure of the SARS-CoV-2 ORF8 protein in an effort to uncover its role in COVID-19 pathogenicity. See this new PNAS publication for a structural exploration that suggests this rapidly evolving accessory protein may play a vital role in immune suppression and evasion. [Abstract]
•	From our graduate student desk, Harvard student Kristen Rodrigues highlighted two publications during the last month, one from the laboratory of William DeGrado at UC California San Francisco that appeared in PNAS in which the authors describe new methods to design multi-domain proteins used to create an allosterically regulated phenol oxidase that responds to the binding of a synthetic porphyrin [Learn more]. A second publication caught her eye in which the laboratories of Stephen Blacklow and Andrew Kruse present work in Science exposing the structural basis of CD19-CD81 B-cell co-receptor complex formation [Learn more].

If you're currently preparing a manuscript, please remember you can publish your datasets in the SBGrid Data Bank along with your PDB record deposit and publication submission to preserve your primary experimental datasets. We also recommend the following boilerplate language in all 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 4 new citations in the month of January, from these SBGrid-member laboratories: Gil Privé of University of Toronto in Journal of Medicinal Chemistry: Fungal-Selective Resorcylate Aminopyrazole Hsp90 Inhibitors: Optimization of Whole-Cell Anticryptococcal Activity and Insights into the Structural Origins of Cryptococcal Selectivity; Stephen Blacklow and Andrew Kruse of Harvard Medical School in Science: Cryo-EM structure of the B cell co-receptor CD19 bound to the tetraspanin CD81; Bing Chen of Boston Children's Hospital in Nature Structural and Molecular Biology: A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent; and Alan Brown at Harvard Medical School in Nature Structural and Molecular Biology: Structures of radial spokes and associated complexes important for ciliary motility.

Software Changes

CCP4 version 7.1.010 is available via version override and includes updates to dials, pointless, mlrda, ccp4cloud, and csheet-bend.

CCPNMR was updated to version 3.0.3.

cryoDRGN version 0.3.1 is available with a new write_starfile.py script to save selected particles as a .star and improvements to cryodrgn analyze.

DIALS is now at version 3.3.0. With this update users can use the dials.estimate_resolution for cc_half for the default resolution analysis, dials.export for on-the-fly bzip2 or gzip compression for mmCIF output. Other changes include dials.find_spots and dials.integrate now have nproc=Auto by default, dials.scale applies a more realistic initial error model, or loads the existing error model if rescaling, dials.stills_process allows for different saturation cutoffs for indexing and integration, dxtbx reads the detector distance from the XTC streams for LCLS Jungfrau data, sets the per-shot gain for the ePix and Jungfrau detectors at LCLS, and allows users to mark format classes as @abstract. Also included is an update to xia2 3.3.0.

IMOD was bumped to version 4.11.1.

LightDock was added at version 0.8.1. New to SBGrid, LightDock is a protein-protein, protein-peptide, and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm.

PEET is now at version 1.15 and includes an update to MATLAB R2020b, new support for hierarchical ascendant classification in clusterPca, and two new programs: MOTL2Relion and relion2MOTL.

Phenix nightly build version 1.19-4092 is the new default.

sbgird-cli is now at version 2.3.1 (note, version 2.14.1 will be released soon). sbgrid-cli is SBGrid's command line installation manager for Mac and Linux. Improvements include multithreaded rsync transfer, selectable installation target path, and network diagnostics for troubleshooting. We will no longer maintain the older v1 command line utility.

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

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007