SBGrid Consortium - News and Events

Newsletter for February 2022

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Published February 2022

Dear Consortium Members and Affiliates,

With this monthly SBGrid recap we are looking ahead to March, hoping for peace and safety for all those in peril. Our news this month: a new CryoEM of membrane proteins webinar mini-series starting March 15th, a reminder about tomorrow's PyMOL webinar, a profile on SITUS software developer Willy Wriggers, a big software push with 17 updates and 2 new titles, 6 new members to welcome, and 3 member publication highlights.

We're retooling our webinar series for the spring with a 6-session mini-series - Cryo-electron microscopy of membrane proteins: from sample to structure - organized in collaboration with Profs. Jamaine Davis of Meharry Medical College, Piotr Sliz of Harvard Medical School, and Patrick Sexton of Monash University. We're excited that such an exceptional lineup of speakers have kindly agreed to participate. Note that we have also updated our Zoom settings to allow for enhanced security, so please be sure to register for this series. Full details at sbgrid.org/webinars/.

Join us tomorrow for the final webinar in our winter software series to hear from Thomas Stewart on what's new in PyMOL. You can also find recordings from our February sessions with Eugene Krissinel providing an overview and advanced introduction to CCP4 Cloud on the SBGrid YouTube channel.

Upcoming SBGrid Webinars

March 1 - Thomas Stewart, Ph.D. - A new approach to visual presets in PyMOL (upcoming in PyMOL 3.0)

SBGrid Spring Mini-series

Cryo-electron microscopy of membrane proteins: from sample to structure.

Mar 15 - Prof. Nieng Yan - The molecular choreography of Cav/Nav channels – A mission impossible by today’s AI

Mar 22 - Sara Weaver, Lisa Eshun-Wilson, and William Nicolas - Sample Preparation: From single particle cryoEM to MicroED, tomography and FIB milling.

Mar 29 - Shaun Rawson and Tom Goddard - Single Particle CryoEM: from data to structure

Apr 5 - Prof. Melanie Ohi - CryoEM analysis of membrane spanning complexes

Apr 12 - Prof. Elizabeth Wright, Caleigh Azumaya, Prof. Craig Yoshioka, Robert Grassucci - Panel discussion led by Melissa Chambers - Regional CryoEM infrastructure in the US

Apr 19 - Prof. Chris Tate -Insights into GPCR activation from cryo-EM structures

See full details and registration here.

For our February SBGrid Tale, we caught up with Willy Wriggers from Old Dominion University in Norfolk Virginia, who contributes SITUS, Sculptor, and TimeScapes to the SBGrid collection. For Wriggers, it's all in the numbers. Whether applied to satellites, race cars, or the structural biology toolbox, numerical computing is where his passions lie. [Read the full story].

We've got a big software push this month, with updates to AlphaFold, APBS, BUSTER, CCPEM, Coot, crYOLO, Dynamo, Geneious, Ligplot+, Maxit, MODELLER, MotionCor2, nmrglue, NMRPipe, ORCA, PHENIX, SAMtools, along with two new titles: AreTomo and ColabFold. See Software Changes below for complete details.

February brought us new members from 6 institutions: Pedro Alzari of Institut Pasteur in France, Navaratnam, Dhasakumar of Yale University School of Medicine, Katherine Hicks from SUNY Cortland, and Limei Zhang from University of Nebraska-Lincoln along with users from Boehringer-Ingelheim, and PAQ Therapeutic. Welcome to our newest members!

Community Announcements

Exploring Structural Database Use in Crystallography: A USNC/Cr Workshop Series: Hosted by US National Committee for Crystallography, National Institute of Standards and Technology, and National Academies of Sciences, Engineering, and Medicine, this series of eleven online workshops - including a presentation by SBGrid - will run from March 21-April 14 with a focus on the use, development, and maintenance of crystallographic and structural databases. Details and Registration

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:

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In a new publication in the Journal of Structural Biology: X, Navtej Toor of the University of California, San Diego reviews recent advances in the study of encapsulin bacterial nanocompartments, made possible by continued innovation in cryo-EM. The authors discuss key components such as the E-loop, cargo-peptide binding site, the five-fold axis channel as well as a flavin-binding pocket that may play a role in iron metabolism.

[Abstract]

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From the laboratory of Stephen Long at Memorial Sloan-Kettering Cancer Center comes a new paper in Science Advances in which the authors describe their investigation into the molecular mechanisms of the proton-activated chloride channel ASOR. From the solved cryo-EM structure of ASOR in an activated conformation, they identify acidic clusters as the primary proton sensors with the ensuing pH-dependent transmembrane metamorphosis directing the ion pore gating.

[Abstract]

•

From our graduate student desk, Harvard student Kristen Rodrigues highlighted a PNAS publication from the NIH laboratory of Anirban Banerjee in which the authors describe their work using X-ray crystallography and molecular dynamics simulations to assess interactions between the human DHHC20 and palmitoyl CoA and report the structure of the pre-catalytic complex. [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 three new citations in the month of February, from these SBGrid-member laboratories: Andres Palencia from the Institute for Advanced Biosciences in Nature: Visualizing protein breathing motions associated with aromatic ring flipping; Michael Eck from Dana-Farber Cancer Institute, contributing to a paper in Cancer Research: A novel HER2-selective kinase inhibitor is effective in HER2 mutant and amplified non-small cell lung cancer; and a multi-institution collaboration including SBGrid contributors at Lawrence Berkeley National Laboratory and SBGrid member Catherine Drennan of MIT in Journal of Inorganic Biochemistry: XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase.

Software Changes

AlphaFold 2.1.2 adds a few new features that users must define explicitly on the command line. For more info see run_alphafold.py --help or Examples at https://sbgrid.org/wiki/examples/alphafold2#examples

APBS version 3.4.0 is out, with a revamped build system.

AreTomo is new to SBGrid at version 1.0.11. AreTomo (Alignment and Reconstruction for Electron Tomography) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.

BUSTER 20220203 has numerous fixes and improvements in the Grade2 restraint dictionary generator.

CCP-EM nightly build 20220125 is now available via version override.

ColabFold version 1.2.0 is another new title. ColabFold is an easy-to-use Notebook-based environment for fast and convenient protein structure predictions.

COOT 0.9.7 is the new default. New features include angles in coot-ligand-validation, "Updating Maps" in the API and GUI, and an option to revert to the 2010 use of Stereo style. Improvements can be seen in better B-factors for added waters, and distance difference filtering for RSR GM restraints along with a number of other bug fixes.

crYOLO 1.8.2 is a minor bug fix release that fixes an error causing crYOLO to use more CPUs than specified by –-num cpu (-nc) and a GLIBC installation problem that occurs when installing crYOLO with CUDA 11.

Dynamo was updated to release 1.1.532 for Linux.

Geneious 2022.0.2 is the new default.

Ligplot+ was bumped to release 2.2.4.

Maxit 11.100 is the new default.

MODELLER 10.2 is a minor update that adds support for Python 3.10.

MotionCor2 was updated to 1.4.7.

nmrglue 0.8 is out with changes to handle data processed with nmrPipe EXT in the z-dimension, guess spectral widths in multi-dimensional Bruker datasets, allow bracket-less text values in JCAMP files and different character encodings in JCAMP files, support reading Sparky .save files and only consider relevant DATATYPEs when reading JCAMP-DX files. You also may notice a new util/xcpy.py module for interfacing nmrglue with Topspin, new autops function options, and improvements to the autops function.

NMRpipe was updated to 20210915 as the new default.

ORCA 5.0.3 is a new bug fix release

PHENIX nightly build 1.20.1-4487 is the new default and adds backwards compatibility for the new solvent masking algorithm and fixes bugs in SHELX HKLF format output, in phenix.dock_and_rebuild where no model is obtained, and for map and model from phenix.douse not aligning.

SAMtools 1.15 adds --min-BQ and --min-MQ options to depth, improved automatic file type detection with view -u or view -1, new optical duplicate marking add regex options for custom coordinates for markdup, new samtools consensus subcommand for generating consensus from SAM, BAM or CRAM files based on the contents of the alignment records, a new samtools view --fetch-pairs option, and a new samtools head subcommand for conveniently displaying the headers of a SAM, BAM, or CRAM file.

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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