easymode

New Title Alert: easymode- a collection of general pretrained networks for cellular cryoET.

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Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection - PubMed The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in…

News Alert: We've updated SBGrid's primary citation to our 2024 Acta Crystallographica paper. We would be grateful if you could use this reference in future manuscripts, preprints, and related work where appropriate.

Read it here: buff.ly/RQ0Ybpx

#SBGrid #Citation

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 Ais, AlphaFold3, Boltzgen, Bowtie2, CellProfiler, ChimeraX, CryoMaskR, CryoSPARC-tools, Foldseek, IsoNet2, Protenix, RDKit, and upside2-md.

More here: buff.ly/SHUsfWz

#SBGrid #Software #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…

Join our software webinar on March 10th to hear from Joshua Mitchell from the Open Molecular Software Foundation on Open Force Field Initiative. '

Tues, March 10, 2026 12:00PM ET
Josh Mitchell
Science Communicator, Open Force Field

Register here: buff.ly/YVCdTmr

#SBGrid #StructuralBiology

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

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.

Read more here: buff.ly/sDiLwk5

#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”

Read more here: buff.ly/M2lX8Ct

#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'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.

Read more here:https://buff.ly/t8tGieS

#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.

Read more here: buff.ly/AnmiV5Y

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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.

Learn more here: buff.ly/cXIXkW8

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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.

Read more here: buff.ly/tY3MqKF

#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.

Learn more here: buff.ly/fVsKsOS

#SBGrid #SBGridSoftware

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.

Learn more here: buff.ly/vuCrtWR

#SBGridSoftware #SBGrid

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.

Learn more here: buff.ly/cZcOmpC

#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.

Read more here: buff.ly/Cjk6R1c

#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).

Learn more here: buff.ly/2ZlZInD

#SBGrid

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.

Learn more here: buff.ly/wCaRFLp

#SBGrid #SBGridSoftware #StructuralBiology

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

Learn more here: buff.ly/2TdjDOE

#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

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.

Learn more here: buff.ly/ormnLqE

#SBGrid #SBGridSoftware #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…

Join our software webinar on February 10th to hear from Alyssa Travitz of the @omsf.io on @openfree.energy: An Open Source Ecosystem for Calculating Free Energies.

Tuesday, February 10, 2026 - 12:00pm ET

Register here: buff.ly/N7AYdjp

#SBGrid #Webinars #StructuralBiology

Structure and immunogenicity of an engineered soluble prefusion-stabilized EBV gB antigen - Nature Communications Epstein–Barr virus (EBV) is a widespread herpesvirus linked to cancer and autoimmune disease. The authors in this work design and characterize a stabilized prefusion form of gB, an essential viral…

SBGrid's eLife paper received a citation in January from @mclellanlab.bsky.social from @utaustin.bsky.social in @nature.com : Structure and immunogenicity of an engineered soluble prefusion-stabilized EBV gB antigen.

Read more here: buff.ly/4nvSiyg

#SBGrid #ScienceMatters

GitHub - mariacarreira/calc_level_ChimeraX: ChimeraX command to predict isosurface levels for 3D density maps ChimeraX command to predict isosurface levels for 3D density maps - mariacarreira/calc_level_ChimeraX

New Title Alert: Calc_level_chimeraX- is a ChimeraX plugin to predict and visualize isosurface levels for 3D density maps.

Learn more here: buff.ly/8tWjgTF

#SBGridSoftware #SBGrid #StructuralBiology

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

#SBGrid #SBGridSoftware #StructuralBiology

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.

Read more here: buff.ly/SLLij5O

#SBGrid

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.

Read more here: buff.ly/D3YfAhc

#SBGrid #ScienceMatters

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

Read more here: buff.ly/zCdXpjI

#SBGrid #ScienceMatters