SBGrid Newsletter: June 2024

Dear Consortium Members and Affiliates,

Our June SBGrid updates includes a reminders about our upcoming and most recent webinars, a software push with nine updates and two new titles, six new members to welcome, and two member publication highlights.

Mark your calendar for the last SBGrid software webinar of the academic season. On July 9th Dennis Brookner from the Hekstra laboratory at Harvard University will introduce us to matchmaps: a general approach to isomorphous, near-isomorphous, and non-isomorphous difference maps for crystallography. [Register here].

You can find a recording of our June webinar with Prof. Darrin York of Rutgers University presenting on Free energy methods in Amber on the SBGridTV YouTube channel [Watch here]

To receive email reminders about upcoming webinars, please be sure to register for the series! Registration here: https://sbgrid.org/webinars/#register

Jul 9: matchmaps - Dennis Brookner

We'll take a break in August and September but will return in October

Webinar topic suggestions welcome!

Oct 8th: qFit - Stephanie Wankowicz

Webinar registration and details

SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Meharry Medical College.

This month's software push includes updates to nine titles including AlphaPulldown, BOWTIE2, cryodrgn, crYOLO, GROMACS, MMseqs2, OpenJDK, Perl, and Warp, along with two new titles: code-server and DRGN-AI. See Software Changes below for complete details.

Six new members joined in the month of June: Naoko Mizuno from the National Institutes of Health, Sagar Bhogaraju from EMBL Grenoble, Pere Puigserver from Dana Farber Cancer Institute, and Yuan He from Johns Hopkins University, and Behnoush Hajian and Guillaume Poncet-Montange from the Broad Institute.  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 Josefina del Mármol of Harvard Medical School that appeared in Nature Communications in which the authors determined the structure of the protein olfactory receptor used in the mosquito nervous system revealing heteromeric membrane receptor, consisting of two different subunits at a unique 3:1 ratio. [Read more]

- Meharry Medical College student KeAndreya Morrison's highlight features a Nature Communications publication on methaqualone. Originally used to treat insomnia and act as a muscle relaxer by enhancing GABA(A) receptor activity, methaqualone was banned due to widespread abuse and addiction. Recent research from the laboratory of Ryan Hibbs from University of California, San Diego revealed its binding sites, offering insights for developing safer sedative drugs. [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 six new citations since our last reporting, from these SBGrid members: James Fraser of University of California San Francisco in eLife: Automated multiconformer model building for X-ray crystallography and cryo-EM; Ryan Hibbs from University of California San Diego in Nature Communications: Structural insights into GABAA receptor potentiation by Quaalude; Daniel Hurdiss from Utrecht University in Nature Communications: Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein; Ramachandran Murali from Cedars-Sinai Medical Center contributing to this publication in Nature: Profiling phagosome proteins identifies PD-L1 as a fungal-binding receptor; Piotr Sliz in Acta Crystallographica Section D: Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection; Alex Vecchio of University of Nebraska-Lincoln/University of Buffalo and Anthony Kossiakoff of University of Chicago in Nature Communications Biology: Structural and biophysical insights into targeting of claudin-4 by a synthetic antibody fragment.

AlphaPulldown 2.0.0b2 is the new default. With 2.0 AlphaPulldown has an updated computing environment, introduces folding_backend, allows the user to pad input matrices to desired number of MSAs and residues to improve speed and avoid unnecessary re-compiling of the AlphaFold neural network, intorduces a new way of modeling with customized structure templates that don't require recalculating features, 

separates post-modelling processes from prediction process, supports full mmseqs2 mode, and adds calculations of average PAE value of interface residues, average plDDT value of interface residues, and of binding energy via pyRosetta value of interfaces to the  analysis_pipeline.

BOWTIE2 was updated to 2.5.4, which adds the --sam-opt-config command line option for toggling SAM Opt flags along with several bug fixes.

code-server 4.90.1 is new to SBGrid. code-server allows users to run VS Code on any machine and access it in the browser.

cryodrgn 3.3.2 makes some improvements to tools used in writing and parsing .star files, as well as addressing a few bugs.

crYOLO 1.9.9 fixes a few bugs.

DRGN-AI is another new title. DRGN-AI turns a collection of single particle cryo-EM images into a continuous ensemble of 3D structures.

GROMACS was updated to 2024-1. Version 2024 allows native use of the Colvars library, simplifying advanced enhanced sampling simulations, reduces artifacts from Lennard-Jones pair interactions on the pressure by a configurable increase of the Verlet buffer, corrects several aspects of the deform option so that simulations with box deformation behave correctly under high shear or when a solid or membrane fractures, and the deform option is now suitable for computing viscosities. There is a new option for hydrogen mass repartitioning in grompp, improvements to AWH, such as better control of the histogram growth factor as well as enabling automatic scaling of the target distribution based on the AWH friction metric, and new options to configure HeFFTe multi-GPU FFT to fine-tune the settings.

MMseqs2 15-6f452 is the new default. MMseqs2 Release 15 brings efficient single query searches with low memory overhead through the new ungapped-prefiltering mode (--prefilter-mode 1). The release also includes improvements to the clustering algorithm along with many other smaller fixes and features.

OpenJDK was updated to JDK 21. OpenJDK Zulu, is the open Java(TM) platform from Azul. The OpenJDK environment includes the Java runtime, compiler, and tools, providing complete runtime support for Java applications.

Perl 5.32.1 contains a number of new modules and fixes.

Warp update v2.0.0dev11 is a bug fix patch.

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

Report software bugs: sbgrid.org/bugs