SBGrid Consortium

SBGrid's eLife paper received a citation in February from Woonghee Lee from University of Colorado Denver in Journal of Biological Chemistry: Modernizing Biomolecular NMR: the POKY Suite.

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#SBGrid #ScienceMatters

New Member Alert: @krishnareddy.bsky.social from @usf.edu joined SBGrid in February. Welcome!!

How signals move through the brain This publication highlight is part of the SBGrid Communities Project focused on science education and demonstrating how structural biology…

Meharry Medical College student Mudiare Ikoba chose to highlight a publication in Nature Communications from the lab of Ed Twomey of The Johns Hopkins University School of Medicine: How signals move through the brain.

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#SBGrid #StructuralBiology

Electric Bacteria: Biological “Power Cords” This publication highlight is part of the SBGrid Communities Project focused on science education and demonstrating how structural biology…

Fisk University student Cariuna Ellison's highlight features a paper from Fengbin (Jerry) Wang of University of Alabama at Birmingham that appeared in Emerging Topics in Life Sciences: Electric Bacteria: Biological “Power Cords”

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#SBGrid #cryoEM #Bacteria

SBGrid's eLife paper received a citation in January from Dhirendra Simanshu at Frederick National Laboratory for Cancer Research in @nature.com Communications

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#SBGrid #StayConnected #ScienceMatters

SBGrid's eLife paper received a citation in January from @drennanlab.bsky.social at @mit.edu in @nature.com : A highly dynamic mononuclear non-heme iron enzyme for the two-step isonitrile biosynthesis.

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#SBGrid #StayConnected #ScienceMatters

SBGrid's eLife paper received a citation in January from Jean-Philippe Julien at @sickkidsto.bsky.social in @Nature Magazine Communications: A stabilized tandem antigen chimera that elicits potent malaria transmission-reducing activity.

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New Member Alert: Martin Schmeing at @mcgill.ca joined SBGrid in January. Welcome!

GitHub - Kuhlman-Lab/ThermoMPNN: GNN trained to predict changes in thermodynamic stability for protein point mutants GNN trained to predict changes in thermodynamic stability for protein point mutants - Kuhlman-Lab/ThermoMPNN

New Title Alert: ThermoMPNN- is a graph neural network (GNN) designed to predict changes in stability for protein point mutants using transfer learning.

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#SBGrid #SBGridSoftware #StructuralBiology

Mechanistic insights into SteAB regulation of cell wall hydrolase RipA in Mycobacterium tuberculosis | mBio Peptidoglycan (PG) is a major component of the bacterial cell wall. A flexible but strong PG mesh encloses the cell, conferring mechanical resistance and preventing cell lysis. This PG mesh is…

SBGrid's eLife paper received a citation in January from @awehenkel.bsky.social , Pedro M. Alzari, and Ahmed Haouz from @pasteur.fr in ASM Journals: Mechanistic insights into SteAB regulation of cell wall hydrolase RipA in Mycobacterium tuberculosis.

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#SBGrid

GitHub - CellArchLab/slabify-et: A CLI tool to segment the lamella slab in cryo-ET volumes A CLI tool to segment the lamella slab in cryo-ET volumes - CellArchLab/slabify-et

New Title Alert: Slabify- is a command-line tool designed for the automatic segmentation of lamella slabs in cryo-electron tomography (cryo-ET) volumes.

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#SBGrid #SBGridSoftware

New Member Alert: Esther Ortega from @cnb-csic.bsky.social joined SBGrid in January. Welcome!

Structural Studies of Fourth-Generation EGFR Inhibitors Reveal Insights into Selective T790M and C797S Targeting Inhibitors targeting mutant EGFR remain a persistent need in combating drug resistance in non-small cell lung cancer. To better understand the molecular factors involved in targeting T790M and C797S…

SBGrid's eLife paper received a citation in January from @heppnerd.bsky.social at @ubuffalo.bsky.social in @acsmedi.bsky.social Letters: Structural Studies of Fourth-Generation EGFR Inhibitors Reveal Insights into Selective T790M and C797S TargetingArticle link copied!

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New Member Alert: Maria Oliva-Blanco from Margarita Salas Center for Biological Research joined SBGrid in January. Welcome!

New Title Alert: MagCalEM- Accurate magnification determination for cryoEM determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximise resolution and enable accurate model building.

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#SBGridSoftware #SBGrid

New Member Alert: Fangyu Liu from UT Southwestern Medical Center joined SBGrid in January. Welcome!

GitHub - polizzilab/LASErMPNN: All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN - polizzilab/LASErMPNN

New Title Alert: LASErMPNN- is an all-atom ligand-conditioned protein sequence design and sidechain packing model that accounts for the presence of small molecules, including hydrogens.

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#SBGridSoftware #SBGrid #StructuralBiology

Synergistic Action of Crystallophore and Imaging‐Crystallophore Enhances the Production and Imaging of Protein Crystals The Imaging-crystallophore (Im-Xo4), a Tb(III) complex substituted by π-conjugated antennas emits in the green and accumulates in the protein crystals, enabling an easy crystal detection using…

SBGrid's eLife paper received a citation in January from Eric Girard at IBS Grenoble in @angewandtechemie.bsky.social: Action of Crystallophore and Imaging-Crystallophore Enhances the Production and Imaging of Protein Crystals.

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#SBGrid #ScienceMatters #StayConnected

GitHub - IsoNet-cryoET/IsoNet2: IsoNet at higher resolution IsoNet at higher resolution. Contribute to IsoNet-cryoET/IsoNet2 development by creating an account on GitHub.

New Title Alert: IsoNet2- a deep-learning software package for simultaneous missing wedge correction, denoising, and CTF correction in cryo-electron tomography reconstructions using a deep neural network trained on information from the original tomogram(s).

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#SBGrid

New Member Alert: In January, @joanafb.bsky.social from @biologiaub.bsky.social joined SBGrid. Welcome!

GitHub - oxpig/ImmuneBuilder: Predict the structure of immune receptor proteins Predict the structure of immune receptor proteins. Contribute to oxpig/ImmuneBuilder development by creating an account on GitHub.

New Title Alert: ImmuneBuilder- is a high-performance deep learning framework developed by the Oxford Protein Informatics Group (OPIG) specifically for predicting the 3D structures of immune receptor proteins.

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#SBGrid #SBGridSoftware #StructuralBiology

New Member Alert: In January, @awehenkel.bsky.social , along with the Image Analysis Hub, under the direction of @jytinevez.bsky.social at @pasteur.fr joined SBGrid. Welcome!!

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: January's software push includes updates to 15 titles -- anvi’o, BioXTAS RAW, ChemEx, CryomaskR, DeepRank-GNN-esm, DSSR, GROMACS, Icecream, IMP, PowerFit, PyEM, RDKit, SRAToolkit, Volume_Seg_Tool, and XDS.

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#SBGridSoftware #Updates

New Member Alert: Daniel Castaño from Biofisika Institute joined SBGrid in January. Welcome!

New Title Alert: Foundry- is a unified framework for protein design that provides tooling and infrastructure for using and training models.

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#SBGrid #SBGridSoftware #StructuralBiology

SBGrid Ecosystem 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 Belmont University.…

If you missed Alice-Roza Eruera's January webinar on Building CryoET Training Workflows Using the SBGrid Ecosystem, you can now find it on our YouTube channel.

Here: buff.ly/CPcy0Nz

#SBGrid #Webinars #ScienceMatters

Installation Manager 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 computing.

Technical Notes: Personal Installation Credentials Users who currently only have access to the SBGrid software collection through a site installation may benefit from access to the collection on personally managed laptops or desktops in the laboratory or at home.

Register here:

A synthetic cell-free pathway for biocatalytic upgrading of formate from electrochemically reduced CO2 - Nature Chemical Engineering Cost-effective, environmentally sustainable and energy-efficient ways to address rising atmospheric CO2 levels are urgently needed. Here the authors combine electrochemical reduction of CO2 to…

SBGrid's eLife paper received a citation in January from @bhartisingal.bsky.social , at @stanford.edu SLAC CryoEM Initiative contributing in @nature.com Chemical Engineering

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#SBGrid #ScienceMatters

GitHub - Rostlab/ConSurf: Evolutionary conservation estimation of residues or nucleotides Evolutionary conservation estimation of residues or nucleotides - Rostlab/ConSurf

New Title Alert: ConSurf- is a bioinformatics tool designed for estimating the evolutionary conservation of amino and nucleic acid positions in protein, DNA, and RNA molecules.

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#SBGrid #SBGridSoftware #StructuralBiology

New Member Alert: James Chen from University of California, San Francisco joined SBGrid in January! Welcome.