SBGrid Consortium

New Member Alert: In September Terje Dokland at the CryoEM Microscopy Facility from University of Alabama at Birmingham joined SBGrid. Welcome!

GitHub - PDB-REDO/AlphaBridge Contribute to PDB-REDO/AlphaBridge development by creating an account on GitHub.

New Title Alert: AlphaBridge- a script that using the output provided by Alphafold3, provides different plots and files useful for the identification of interacting interfaces.

Learn more here: buff.ly/gVZhhhj

#SBGrid #SBGridSoftware #StructuralBiology

Getting rid of arsenic SBGrid member William Clemons Jr. looks at how the ArsA enzyme reshapes itself to capture and expel toxic arsenic.

Getting rid of arsenic: a publication from the lab of William Clemons Jr. from @caltech.edu that reveals how the ArsA enzyme reshapes itself to capture and expel toxic arsenic, providing a structural blueprint for microbial survival.

Read more here: buff.ly/OC5nXeF

#SBGrid #Arsenic

New Member Alert: @tbeyett.bsky.social at Emory University School of Medicine joined SBGrid in September. Welcome!

Investigating antibiotic characteristics from the computer SBGrid member Jens Meiler uses Rosetta to design antibiotic peptides called lanthipeptides with antibiotic properties.

@caltech.edu doctoral student Vida Robertson highlighted a publication from Jens Meiler, from @vanderbilt.edu, who describes using Rosetta to design antibiotic peptides called lanthipeptides with antibiotic properties.

Read more here: buff.ly/d6k8HvB

#SBGrid #NMR #ProteinDesign

Prodigy Webserver Home

New Title Alert: PRODIGY- a collection of web services focused on the prediction of binding affinity in biological complexes as well as the identification of biological interfaces from crystallographic one.

Learn more here: buff.ly/mrqcL3V

#SBGrid #SBGridSoftware #StructuralBiology

SBGrid Consortium - Member Tale - Gira Bhabha - Johns Hopkins University The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…

Our member tale for October features Gira Bhabha. Now at @jhu.edu Bhabha's lab is joined w/ Damian Ekiert, her partner in science & in life, where she studies MCE proteins in tuberculosis & the interactions between microsporidia parasites & host cells.

Read more here: buff.ly/bz0eCIE

#SBGTales

Structural Basis for Postfusion-Specific Binding to the Respiratory Syncytial Virus F Protein by the Canonical Antigenic Site I Antibody 131–2a The respiratory syncytial virus (RSV) fusion (F) protein is a major target of antiviral antibodies following natural infection or vaccination and is responsible for mediating fusion between the viral…

SBGrid's eLife paper received a citation in August from @joostsnijder.bsky.social from @utrechtuniversity.bsky.social in @pubs.acs.org Infectious Diseases.

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#SBGrid #StayConnected #ScienceMatters

The bacterial ESCRT-III PspA rods thin lipid tubules and increase membrane curvature through helix α0 interactions | PNAS The phage shock protein A (PspA), a bacterial member of the endosomal sorting complexes required for transport (ESCRT)-III superfamily, forms rod-s...

SBGrid's eLife paper received a citation in August from @sachsegroup.bsky.social of @fz-juelich.de in @pnas.org : The bacterial ESCRT-III PspA rods thin lipid tubules and increase membrane curvature through helix α0 interactions.

Read more here: buff.ly/b6glCsD

#SBGrid #ScienceMatters

SBGrid's eLife paper received a citation in August from @mclellanlab.bsky.social from @utlonghorns.bsky.social in @jem.org : Repertoire, function, and structure of serological antibodies induced by the R21/Matrix-M malaria vaccine.

Read more here: buff.ly/B47CZBG

#SBGrid #StayConnected

New Member Alert: Jiankun Lyu from @rockefelleruniv.bsky.social joined SBGrid in August. Welcome!

Mouse monoclonal antibodies against Clostridioides difficile toxins TcdA and TcdB target diverse epitopes for neutralization | Infection and Immunity The growing burden of Clostridioides difficile infection (CDI) on healthcare in the United States continues to drive investigation of new strategies to treat or prevent the disease. It is considered…

SBGrid's eLife paper received a citation in August from @bordenlacy.bsky.social from @vubasicsciences.bsky.social in Infection and Immunity: Mouse monoclonal antibodies against Clostridioides difficile toxins TcdA & TcdB target diverse epitopes for neutralization.

Read more here: buff.ly/nneShoz

New Member Alert: In August, Dvir Harris from Technion - Israel Institute of Technology joined SBGrid. Welcome!

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SBGrid's eLife paper received a citation in August from @heppnerd.bsky.social from @sunyofficial.bsky.social at Buffalo in Journal of Medicinal Chemistry: Profiling and Optimizing Targeted Covalent Inhibitors through EGFR-Guided Studies.

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#SBGrid #ScienceMatters

GitHub - rrwick/Unicycler: hybrid assembly pipeline for bacterial genomes hybrid assembly pipeline for bacterial genomes. Contribute to rrwick/Unicycler development by creating an account on GitHub.

New Title Alert: Unicycler- an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser.

Learn more here: buff.ly/DcKYVGL

#SBGrid #StructuralBiology #Software

De novo design and structure of a peptide–centric TCR mimic binding module T cell receptor (TCR) mimics offer a promising platform for tumor-specific targeting of peptide–major histocompatibility complex (pMHC) in cancer immunotherapy. In this study, we designed a de novo…

SBGrid's eLife paper received a citation in August from K. Christopher Garcia from @stanford.edu School of Medicine in @science.org: De novo design and structure of a peptide-centric TCR mimic binding module.

Read more here: buff.ly/1UxK5Ka

#SBGrid #StayConnected

New Member Alert: Weiwei Wang from UT Southwestern Medical Center joined SBGrid in August. Welcome!!

Copper acquisition in Bacillus subtilis involves Cu(II) exchange between YcnI and YcnJ The transition metal copper (Cu) is biologically essential across all three domains of life. Several Cu-dependent proteins and enzymes produced by the Gram-positive bacterium Bacillus subtilis have…

SBGrid's eLife paper received a citation in August from @fisherlab.bsky.social at @wesleyanuniversity.bsky.social in Journal of Biological Chemistry: Copper acquisition in Bacillus subtilis involves Cu(II) exchange between YcnI and YcnJ.

Read more here: buff.ly/myITTv8

#SBGrid #ScienceMatters

GitHub - A4Bio/E3-CryoFold Contribute to A4Bio/E3-CryoFold development by creating an account on GitHub.

New Title Alert: E3-CryoFold- a deep learning framework for automating the determination of three-dimensional atomic structures from high-resolution cryo-electron microscopy (Cryo-EM) density maps.

Learn more here: buff.ly/CDzcfBp

#SBGrid #StructuralBiology #Software

Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation Slabicki et al. use a high-throughput reporter screen to identify zinc finger proteins degraded by glutarimide compounds via CRBN. Structural and mutational analyses reveal substrate-specific CRBN…

SBGrid's eLife paper received a citation in August from Eric Fischer from @danafarber.bsky.social in @cp-molcell.bsky.social: Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation.

Read more here: buff.ly/aU3rwJh

#SBGrid #ScienceMatters

GitHub - UNITES-Lab/CryoNeRF Contribute to UNITES-Lab/CryoNeRF development by creating an account on GitHub.

New Title Alert: CryoNeRF- a computational tool for homogeneous and heterogeneous (conformational and compositional) cryo-EM reconstruction in Euclidean 3D space.

Learn more here: buff.ly/a1BZZx5

#SBGrid #StructuralBiology #Software

Structural basis for anaerobic alkane activation by a multisubunit glycyl radical enzyme | PNAS X-succinate synthases (XSSs) are glycyl radical enzymes (GREs) that catalyze the addition of hydrocarbons to fumarate via radical chemistry, thereb...

SBGrid's eLife paper received a citation in August from @drennanlab.bsky.social from @mit.edu in @pnas.org: Structural basis for anaerobic alkane activation by a multisubunit glycyl radical enzyme.

Read more here: buff.ly/Reqb8UR

#SBGrid #StayConnected

SBGrid Consortium - Software Updates The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…

August's software push includes updates to over 20 titles including ACPyPE, AlphaPulldown, Boltz, CCP-EM, ChimeraX, CryoDRGN, Doppio, fpocket, Geneious, Gnuplot, ISOLDE, IsoNet, MDAnalysis, MemBrain-seg, Napari, NMRFx-Analyst, and many more.

More information here: buff.ly/KhZw2Tb
#SBGrid #Software

Real-time capture of σN transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding - Nature Communications Bacterial transcription with σN requires activation by specialized AAA+ ATPases. Here, the authors visualize transient structural intermediates and engineer a biochemical assay to show that these…

SBGrid's eLife paper received a citation in August from Seth Darst of @rockefelleruniv.bsky.social in @nature.com: Real-time capture of σN transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding.

Read more here: buff.ly/Dt2D4dY

#SBGrid #Science

Stopping Ribosomes in Action! SBGrid member Chi-Min Ho uses cryo-electron tomography to map malaria’s ribosomes at work.

Stopping Ribosomes in Action!: a publication highlight from @keandreyam.bsky.social featuring the lab of @cmholab.bsky.social of @columbiauniversity.bsky.social & colleagues.

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#SBGrid #CryoET

Clonotype-enriched somatic hypermutations drive affinity maturation of a public human antibody targeting an occluded sarbecovirus epitope Rao et al. demonstrate that convergent somatic hypermutations in the light chain, enriched within a sarbecovirus-specific public antibody clonotype, drive affinity maturation. This antibody targets a…

SBGrid's eLife paper received a citation in August from @gogo-science.bsky.social from Icahn School of Medicine at Mount Sinai in @cellpress.bsky.social.

Read more here: buff.ly/gTkJDtd

#SBGrid #StayConnected

New Member Alert: @dvorinlab.bsky.social from @bostonchildrens.bsky.social joined SBGrid in August. Welcome!!

Structural insights into rare, heritable neurodegeneration SBGrid member David Eliezer shows the aggregated structures caused by a key mutation in mitochondrial proteins that cause…

Structural Insights into rare, heritable neurodegeneration: a publication highlight from @caltech.edu doctoral student Vida Robertson in @nature.com Communications from SBGrid member David Eliezer's lab out of the @weillcornell.bsky.social

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#SBGrid #StructuralBiology

Webinars The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…

Our monthly software webinars will resume in October with @alisiafadini.bsky.social and @minhuanli.bsky.social covering AlphaFold as a Prior: Guiding Protein Structure Prediction Using Experimental Data with ROCKET.

Tuesday, October 14, 2025 at 12:00pm ET
Register here: buff.ly/uLlQGVr

#SBGrid

GitHub - BEAM-Labs/FoldBench Contribute to BEAM-Labs/FoldBench development by creating an account on GitHub.

New Title Alert: FoldBench- a comprehensive all-atom benchmark for biomolecular structure prediction that spans proteins, nucleic acids, ligands, and six major interaction types.

Learn more here: buff.ly/NE4INJW

#SBGrid #SBGridSoftware #StructuralBiology