SBGrid Consortium

GitHub - Kuhlman-Lab/ThermoMPNN-D: Extension of ThermoMPNN for double mutant predictions Extension of ThermoMPNN for double mutant predictions - Kuhlman-Lab/ThermoMPNN-D

New Title Alert: ThermoMPNN-D- is a Siamese neural network designed to predict stability changes from protein double point mutations.

Learn more here: buff.ly/rogxB7G

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The Stories Antibodies Tell Jean-Philippe Julien from The Hospital for Sick Children interrogate antibodies that arise from natural infections and vaccine trials.

Our January member tale features Jean-Philippe Julien from @sickkidsto.bsky.social in Toronto, who interrogates antibodies in the science of global heath, following their stories to guide interventions against infectious diseases like malaria.

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#SBGridTales

SBGrid Consortium For structural biologists, by structural biologists! The SBGrid TV channel was developed with participation from many members of the structural biology community. We welcome suggestions for topics to…

If you missed Alice-Roza Eruera's January webinar on Building CryoET Training Workflows Using the SBGrid Ecosystem, we will have the video posted to the SBGrid YouTube channel soon.

You can subscribe at buff.ly/RTDvlIb to receive alerts when new videos are added.

#SBGrid #Webinars #ScienceMatters

Structural organization of p62 filaments and the cellular ultrastructure of calcium-rich p62-enwrapped lipid droplet cargo - Nature Communications The selective autophagy receptor p62/SQSTM1 is organized in a structured double helical filament in vitro, the cryo-electron tomographic images in ATG5 knockdown conditions reveal Ca-rich layers of…

SBGrid's eLife paper received a citation in December from @sachsegroup.bsky.social from @fz_juelich in @natcomms.nature.com: Structural organization of p62 filaments and the cellular ultrastructure of calcium-rich p62-enwrapped lipid droplet cargo.

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How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity Structural snapshots reveal how ATP and dATP reposition class III RNR cone domains to control substrate binding and activity.

SBGrid's eLife paper received a citation in December from Catherine Drennan from @mit.edu in Science Advances: How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity.

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New Member Alert: In December, Paul Seidler from @usc.edu joined SBGrid. Welcome!!

Distinct quaternary states, intermediates, and autoinhibition during loading of the DnaB-replicative helicase by the phage λP helicase loader Abstract. Replicative helicases need loader proteins to assemble at DNA replication origins. Multiple copies of the bacteriophage λP (P) loader bind and lo

SBGrid's eLife paper received a citation in December from David Jeruzalmi atThe City College of New York in @narjournal.bsky.social

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New Member Alert: Vera Moiseenkova-Bell from @isbupenn.bsky.social joined SBGrid in December!. Welcome!!

GitHub - ccameron/REPIC: REliable PIcking by Consensus (REPIC) - an ensemble learning methodology for cryo-EM particle picking REliable PIcking by Consensus (REPIC) - an ensemble learning methodology for cryo-EM particle picking - ccameron/REPIC

New Title Alert: REPIC- REliable PIcking by Consensus (REPIC) is a consensus methodology for harnessing multiple cryogenic-electron microscopy (cryo-EM) particle picking algorithms.

Learn more here: buff.ly/cCqyNHx

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Transcription co-inhibition alters drug resistance evolution and enhances Mycobacterium tuberculosis clearance from granulomas - Nature Microbiology Targeting two distinct steps of the transcription process yields synergistic antibiotics that kill non-replicating Mycobacterium tuberculosis and reduce drug resistance.

SBGrid's eLife paper received a citation in December from Elizabeth Campbell from @rockefeller.edu in @natmicrobiol.nature.com: Transcription co-inhibition alters drug resistance evolution and enhances Mycobacterium tuberculosis clearance from granulomas.

Read more here: buff.ly/6yvUxRw

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New Title Alert: cryomaskR- is a desktop application that provides WYSIWYG mask generation for cryo-electron microscopy data analysis.

Learn more here: buff.ly/MC0uNqR

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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 January software webinar will feature Sliz Lab postdoc Alice-Roza Eruera on Building CryoET Training Workflows Using the SBGrid Ecosystem. Be sure to join us on January 13th!

Register here: buff.ly/wwNF6Zh

#SBGrid #StructuralBiology #Webinars

Functional and structural analyses of UbcH5 mutants with enhanced binding to the E3 ubiquitin ligase CHIP The E3 ubiquitin ligase CHIP ubiquitinates substrates in chaperone-dependent or -independent manners. Structural studies, particularly by cryo-electro…

SBGrid's eLife paper received a citation in November from Rick Page from Miami University Ohio in Biochemical and Biophysical Research Communications: Functional and structural analyses of UbcH5 mutants with enhanced binding to the E3 ubiquitin ligase CHIP.

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GitHub - rs-station/meteor: bringing you the best difference maps bringing you the best difference maps. Contribute to rs-station/meteor development by creating an account on GitHub.

New Title Alert: meteor- a tool for computing crystallographic difference maps that specializes in robust identification of weak signals from minor populations such as bound ligands or time-resolved experimental changes.

Learn more here: buff.ly/bgJYF9N

#SBGrid #SBGridSoftware #StructuralBiology

SBGrid's eLife paper received a citation in November from @palencialab.bsky.social from @ugrenoblealpes.bsky.social in @natcomms.nature.com Hierarchical folding-upon-binding of an intrinsically disordered protein.

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#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…

Technical Notes: This month's software push includes updates to BioEmu, BoltzGen, ChimeraX, DOCK, Google Cloud SDK, HADDOCK3, NAMD, OpenFold, ORCA, pytom-match-pick, pyTME, SamTOOLS, Schrödinger 2025-3 and 2025-4, and Topaz.

More information here: buff.ly/lgtNHCd

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Structures of human organellar SPFH protein complexes - Nature Communications SPFH proteins oligomerize with distinct stoichiometries in all kingdoms of life. Here, Gao et al. determine cryo-EM structures to elucidate the compositions of the ER-resident Erlin and the…

SBGrid's eLife paper received a citation in November from@sshaolab.bsky.social from @harvardmed.bsky.social in@natcomms.nature.com : Structures of human organellar SPFH protein complexes.

Read more here: buff.ly/lbuE0ZR

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New Member Alert: Cesar Santiago from @cnb-csic.bsky.social in Spain joined SBGrid in November. Welcome!

Human RPA is an essential telomerase processivity factor for maintaining telomeres Telomerase counteracts telomere shortening by repeatedly adding DNA repeats to chromosome ends. We identified the replication protein A (RPA) heterotrimer as a telomerase processivity factor critical…

SBGrid's eLife paper received a citation in November from @cijilim.bsky.social from University of Wisconsin-Madison in @science.org : Human RPA is an essential telomerase processivity factor for maintaining telomeres.

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#SBGrid #Stayconnected

GitHub - yehlincho/Protein-Hunter Contribute to yehlincho/Protein-Hunter development by creating an account on GitHub.

New Title Alert: Protein-Hunter- a tool for exploiting structure hallucination within diffusion for protein design. A fast, fine-tuning-free framework for de novo protein design.

Learn more here: buff.ly/DrCDsKH

#SBGrid #StructuralBiology #SBGridSoftware

SBGrid's eLife paper received a citation in November from Andrew Kruse from @harvardmed.bsky.social in @pnas.org : Conformational regulation of two essential activators of bacterial cell elongation.

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New Member Alert: Wayne Patrick from @vicuniwgtn.bsky.social joined SBGrid in November. Welcome!

Human antibody targeting of coronavirus spike S2 subunit is associated with protection mediated by Fc effector functions | Journal of Virology Bats and pangolins are natural reservoirs of betacoronaviruses (β-CoVs) and continue to pose a significant risk for future outbreaks through zoonotic transmissions. This highlights the need for…

SBGrid's eLife paper received a citation in November from Jean-Philippe Julien from
@sickkidsto.bsky.social in Journal of Virology.

Read more here: buff.ly/08Bai02

#SBGrid #ScienceMatters

CryoSiam Documentation Welcome to the official documentation for the CryoSiam method. This guide will help to use this tool effectively.

New Title Alert: CryoSiam- a self-supervised deep learning framework that works on dense and subtomogram levels.

Learn more here: buff.ly/xt1uGJt

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Structural Insights into De Novo Promoter Escape by Mycobacterium tuberculosis RNA Polymerase - Nature Communications Promoter escape is a key step in bacterial transcription and a target of the antibiotic rifampicin. Here, the authors use cryo-EM to explore this step, finding seven structural intermediates of M.…

SBGrid's eLife paper received a citation in November from Seth Darst at @rockefelleruniv.bsky.social in @nature.com Communications: Structural Insights into De Novo Promoter Escape by Mycobacterium tuberculosis RNA Polymerase.

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GitHub - swing-research/CryoLithe Contribute to swing-research/CryoLithe development by creating an account on GitHub.

New Title Alert: CryoLithe- a supervised machine learning method to directly reconstruct the tomogram from aligned cryo-ET tilt series. The methods is trained on real measurements using FBP+cryo-CARE+IsoNet reconstructions as the reference.

Learn more here: buff.ly/3jxoax3

#SBGrid #Software

Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization Introduction: Numerous X-ray crystal structures of the c-Src SH3 domain have provided a large sampling of atomic-level information for this important signaling domain. Multiple crystal forms have…

SBGrid's eLife paper received a citation in November from Titus Boggon from Yale University in Protein and Peptide Letters: Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization.

Read more here: buff.ly/diXPL4b

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cryoCAT: Contextual Analysis Tools for cryo electron tomography — cryoCAT 0.2.2 documentation Site Navigation

New Title Alert: CryoCAT- an open source, GPL-3.0+ licensed library providing contextual analysis tools for cryo electron tomography and subtomogram averaging.

Learn more here: buff.ly/ug59jUR

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The far extracellular CUB domain of the adhesion GPCR ADGRG6/GPR126 is a key regulator of receptor signaling | PNAS Adhesion G protein–coupled receptors (aGPCRs) transduce extracellular adhesion events into cytoplasmic signaling pathways. ADGRG6/GPR126 is an aGPC...

SBGrid's eLife paper received a citation in November from @demet-arac.bsky.social from the University of Chicago in @pnas.org : The far extracellular CUB domain of the adhesion GPCR ADGRG6/GPR126 is a key regulator of receptor signaling.

Read more here: buff.ly/PPDb9qD

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GitHub - YangLab-SDU/CryoAtom: From cryo-EM density map to atomic structure From cryo-EM density map to atomic structure. Contribute to YangLab-SDU/CryoAtom development by creating an account on GitHub.

New Title Alert: CryoAtom- is a software that automatically constructs full-atom 3D structural models of proteins based on cryo-EM density maps and sequence information.

Learn more here: buff.ly/gjVyH1m

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