SBGrid Consortium - News and Events

Newsletter for May 2022

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Published May 2022

Dear Consortium Members and Affiliates,

SBGrid news for May includes a software push with 8 updates and 2 new titles, 3 new members to welcome, two positions postings from member labs, and four member publication highlights.

For our May software push, you'll find updates to CCP4, DeepEMhancer, IsoNet, Jalview, PyEM, Schrödinger, Relion, and R along with two new titles: seaview and TomosegmemTV . See Software Changes below for complete details.

Three new members joined in the month of May: Steven Damo of Fisk University, Nicholas Polizzi of Dana Farber Cancer Institute, and Nested Therapeutics. Welcome to our newest members!

Community Announcements

CLOUD / HPC SOLUTIONS EXPERT

SBGrid, Harvard Medical School

SBGrid is seeking a full-time Cloud/HPC Solutions Expert to support SBGrid deployment in HPC and Cloud environments for our biotech, pharmaceutical, and academic members. The Cloud/HPC Solutions Expert will join our technical team in a hybrid position that marries customer service with a strong technical foundation to develop, implement, and oversee adoption of best practices. [Details and how to apply]

HEAD OF BIOCHEMISTRY

Seqirus

Seqirus is seeking a structural biologist with a focus on viral proteins. The Head of Biochemistry will build a world class Biochemistry group and lead vaccine antigen design and early process development for protein- and mRNA-based vaccine discovery. [Details and how to apply]

Member Publications Highlights

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:

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A new manuscript in Bioinformatics from the laboratory of Anna Pyle at Yale University introduces AMIGOS III, a PyMOL plugin for pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. AMIGOS III improves upon its predecessor, AMIGOS II, by incorporating the ability to calculate the pseudo-torsion angles etaʹ and thetaʹ for both DNA and RNA structures and by introducing pseudo-torsion angle visualization for DNA and nucleic acid worm visualization.

[Abstract]

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Bing Chen of Boston Children’s Hospital published a comment in Nature Methods highlighting the potent role that structural biology techniques have played in battling SARS-CoV-2, with special emphasis on the rapid evolution of cryo-EM technology that started in 2013. From the structure determination of a key enzyme in SARS-CoV-2 viral replication, the main protease (ProM), less than two weeks after the release of the first viral genomic sequence, to several additional structures of spike (S)-protein complexes shortly thereafter, structure biology methods have emerged as vital tools in the fight against human pathogens. [Abstract]

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In a fascinating Protein & Cell recollection, Professor Jia-huai Wang of Dana-Farber Cancer Institute reminisces about the early days of structural biology at the Beijing Institute of Biophysics. The article serves a moving tribute to his late mentor, Professor Zhengjiong Lin (1935–2022), who guided Wang during the nascent days of his structural biology career. [Abstract]

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From our graduate student desk, Harvard student Kristen Rodrigues highlighted an Immunity publication from SBGrid members Michel Nussenzweig, Rockefeller University and Christopher Barnes, Stanford University in which the authors report on their search for new neutralizing epitopes using NTD-specific probes that revealed conserved neutralizing epitopes outside the NTD supersite. [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 six new citations in the month of May, from these SBGrid-member laboratories: Frank van Kuppeveld of University Utrecht in Science: An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variants of concern; Yang Gao of Rice University in Nature Communications: In crystallo observation of three metal ion promoted DNA polymerase misincorporation; Michael Eck of Dana Farber Cancer Institute in Nature Communications: Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors; Juan Fontecilla-Camps of IBS Grenoble Chemical Reviews: Quinolinate Synthase: An Example of the Roles of the Second and Outer Coordination Spheres in Enzyme Catalysis; Alan Brown from Harvard Medical School in Nature Structural and Molecular Biology: Ciliary central apparatus structure reveals mechanisms of microtubule patterning; David Taylor from University of Texas at Austin in Nature Communications: Structural rearrangements allow nucleic acid discrimination by type I-D Cascade

Software Changes

CCP4 8 represents a complete infrastructure overhaul for Qt5 and Python 3.7 frameworks and the integration of Alphafold models for molecular replacement. Version 8 also includes several new components: Modelcraft 2.2.3 for building protein, nucleic acid chains, carbohydrates, general ligands, and buffer molecules in both X-ray and EM maps; IRIS for per-residue validation metrics for entire protein chains; and PAIREF, a tool to estimate the optimal high-resolution cut-off.

DeepEMhancer is now available as an alternative installation for CUDA 10.0 compatible systems. Users can access this version via version override.

IsoNet with Cuda 10 was pushed out to solve a compatibility error encountered by one user. This version is available via version override.

Jalview 2.11.2.1 solves a problem with running Jalview on M1 Macs.

PyEM 20220427 is the new default.

Relion 4.0-beta2 is available via version override

R 4.1.3 was pushed out and is available via version override.

AND speaking of version overrides, in case you are unfamiliar with the necessary commands, see the Overriding Software Versions page on our wiki.

Schrödinger release 2022-2 is now available for those labs in North America that opted in for support.

Seaview was added to SBGrid at version 5.0.4. Seaview is a multi-platform, graphical user interface for multiple sequence alignment and molecular phylogeny.

TomosegmemTV is also new to SBGrid from the laboratory of José-Jesús Fernández. TomosegmemTV is a software package for segmenting membranes in tomograms based on a Gaussian-like model of membrane profile, a local differential structure approach, and anisotropic propagation of the local structural information using the tensor voting algorithm.

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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