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SBGrid Consortium

@sbgrid.bsky.social

1.5K followers 190 following 370 posts

Harvard-based consortium curating structural biology (CryoEM Crystallography NMR Tomography) software, hosting educational webinars, supporting reproducibility, validation, reprocessing of data, & access to scientific resources sbgrid.org / biogrids.org

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SBGrid Consortium @sbgrid.bsky.social · 5h

New Title Alert: prodigy-lig- is a structure-based method for the prediction of binding affinity in protein-small ligand (such as drugs or metabolites) complexes.

Learn more here: buff.ly/1PYlZIe

#SBGrid #SBGridSoftware #StructuralBiology

GitHub - haddocking/prodigy-lig: Prediction of Protein-Small molecule binding affinities

Prediction of Protein-Small molecule binding affinities - haddocking/prodigy-lig

SBGrid Consortium @sbgrid.bsky.social · 6h

September's software push includes updates to- AlphaPulldown, Boltz, ChemEM, ColabDesign, cryoDRGN, EMReady2, GROMACS, HADDOCK, NMRFxAnalyst, NMRFxStructure, PowerFit, PyTom-Match-Pick, R, RDKit, RFDiffusion, Scipion, SSDraw, Starparser, Topaz, Volume_Seg_Tool, & Warp.

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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…

SBGrid Consortium @sbgrid.bsky.social · 7h

Job posting: Research Associate - SBGrid a computationally minded PhD structural biologist interested in advancing research through installing, curating, validating, & benchmarking the software that underpins macromolecular structure determination.
academicpositions.harvard.edu/postings/15185

HMS - Research Associate in SBGrid, Department of Biological Chemistry and Molecular Pharmacology

We invite applications for a Research Associate position in SBGrid at Harvard Medical School. This annually appointed academic role advances discovery in structural biology by curating, validating, an...

academicpositions.harvard.edu

SBGrid Consortium @sbgrid.bsky.social · 1d

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

SBGrid Consortium @sbgrid.bsky.social · 1d

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

GitHub - PDB-REDO/AlphaBridge

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

SBGrid Consortium @sbgrid.bsky.social · 2d

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

Getting rid of arsenic

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

SBGrid Consortium @sbgrid.bsky.social · 5d

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

SBGrid Consortium @sbgrid.bsky.social · 5d

@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

Investigating antibiotic characteristics from the computer

SBGrid member Jens Meiler uses Rosetta to design antibiotic peptides called lanthipeptides with antibiotic properties.

SBGrid Consortium @sbgrid.bsky.social · 6d

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

Prodigy Webserver

SBGrid Consortium @sbgrid.bsky.social · 6d

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

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…

SBGrid Consortium @sbgrid.bsky.social · 8d

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

Read more here: buff.ly/0VRRJZz

#SBGrid #StayConnected #ScienceMatters

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 Consortium @sbgrid.bsky.social · 9d

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

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 Consortium @sbgrid.bsky.social · 12d

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

Repertoire, function, and structure of serological antibodies induced by the R21/Matrix-M malaria vaccine | Journal of Experimental Medicine | Rockefeller University Press

In this study, McDaniel et al. examine the molecular features of the antibody response to the R21/Matrix-M malaria vaccine in malaria-naïve volunteers. R21

SBGrid Consortium @sbgrid.bsky.social · 13d

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

SBGrid Consortium @sbgrid.bsky.social · 14d

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

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 Consortium @sbgrid.bsky.social · 15d

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

SBGrid Consortium @sbgrid.bsky.social · 16d

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.

Read more here: buff.ly/VwDYVh2

#SBGrid #ScienceMatters

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SBGrid Consortium @sbgrid.bsky.social · 16d

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

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.

SBGrid Consortium @sbgrid.bsky.social · 19d

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

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 Consortium @sbgrid.bsky.social · 20d

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

SBGrid Consortium @sbgrid.bsky.social · 21d

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

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 Consortium @sbgrid.bsky.social · 22d

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

GitHub - A4Bio/E3-CryoFold

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

SBGrid Consortium @sbgrid.bsky.social · 23d

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

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 Consortium @sbgrid.bsky.social · 26d

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

GitHub - UNITES-Lab/CryoNeRF

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

SBGrid Consortium @sbgrid.bsky.social · 27d

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

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...