#sbgrid — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #sbgrid, aggregated by home.social.
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SBGrid's eLife paper received a citation in July from Chi-Min Ho from Columbia University in Cell: Structural basis for host membrane binding and remodeling by invading malaria parasites.
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New Title Alert: copick- is a cross-platform, storage-agnostic and server-less dataset API for cryoET datasets. Access to the data is provided through an object-oriented API that abstracts away the underlying storage using the fsspec-family of libraries.
More here: https://copick.github.io/
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Community Announcement: Upcoming events from our partners at Instruct-ERIC
Instruct-ERIC Webinar Series: Structure Meets Function 49
September 15, 2026 | VirtualJoin to hear an overview of services available through 2 facilities that recently joined Instruct-ERIC: the European XFEL and Forschungszentrum Jülich.
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Welcome to Vina Nguyen of Lipscomb University, a new contributor to our student desk! Vina chose to highlight a publication from the laboratory of Mihnea Bostina at University of Otago that appeared in Journal of Molecular Biology in which the authors describe how the newly found structure of Bas18 provides a reference tool to bacterial viruses, with potential uses in therapeutics, vaccines, and food safety.
Read more here: https://medium.com/sbgrid-community-news/small-viruses-can-have-a-big-impact-on-human-health-56cdb2f4815a
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SBGrid's eLife paper received a citation in July from Eric Fischer from Dana-Farber Cancer Institute in Science: Degron-independent recruitment of KAT2A expands the target space of CRBN molecular glues.
More here: https://www.science.org/doi/abs/10.1126/science.aef5391
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Technical Notes: July's software push includes updates to 20 titles --- BCFtools, Blast+, Chimera, CcpNmr Analysis, Fiji, GROMACS, Icecream, IMOD, LigPlot+, MODELLER, NMRPipe, OpenEye, OpenFold3, RDKit, SAMtools, Schrödinger, Scipion, TEMPy-ReFF, tomoDRGN, and Warp.
More here: https://sbgrid.org/software/recent/archive/2026/07/
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Fisk University student Cariuna Ellison's highlight features a publication from Youxing Jiang at UT Southwestern Medical Center that appeared in Nature Communications and describes their investigation of a small molecule, NC1, that activates a cancer ion channel, leading to overload and cancer cell death.
Read more here: https://medium.com/sbgrid-community-news/open-the-floodgates-how-nc1-makes-trpm4-destroy-cancer-cells-fc20d3b2a003
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New Title Alert: Leopard-EM (Location & oriEntatiOn of PARticles found using two-Dimensional tEmplate Matching) is a python package for running two-dimensional template matching (2DTM) on cryo-EM images.
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We finished our 2025-2026 Software Webinar season in July with a presentation from Mart So-Last on Ais, Pom, and easymode. In case you missed it, you can find the recorded version on the SBGridTV YouTube channel:
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SBGrid's eLife paper received a citation in June from Yunsun Nam from University of Texas Southwestern Medical Center in Nature: Substrate selectivity of the human RNA m5C methyltransferase NSUN2.
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SBGrid's eLife paper received a citation in June from Ed Twomey from The Johns Hopkins University School of Medicine in PNAS: Cryo-EM reveals a right-handed double-helix dimer architecture of PCDH15.
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New Title Alert: warpylib- is a Python library replicating core functionality from [WarpLib](https://github.com/warpem/warp), a C# framework for cryo-electron tomography (cryo-ET) data processing. Built on PyTorch for GPU acceleration and automatic differentiation.
More here: https://github.com/warpem/warpylib
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SBGrid's eLife paper received a citation in June from Miguel Leung from the Hubrecht Institute in Nature: Cytoplasmic lattices are megadalton storage complexes in mammalian oocytes.
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SBGrid's eLife paper received a citation in June from Mark Lemmon from Yale University School of Medicine in Biochemical Journal: An S752D activation loop mutation dynamically primes Muscle-Specific Kinase for activation.
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SBGrid's eLife paper received a citation in June from Jennifer Cash from University of California, Davis in the Journal of Biological Chemistry: The Rho guanine-nucleotide exchange factor P-Rex2 exhibits structural and regulatory features distinct from the related RhoGEF P-Rex1.
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Community Announements: Upcoming events from our partners at Instruct-ERIC
Instruct-ERIC hands-on workshop on: Advanced cryo-FIB-SEM methods
Application deadline: July 1
Nov 9-13, 2026 | Heidelberg, Germany
Organized by the EMBL Imaging Centre -
New Title Alert: CryoZeta- is a de novo macromolecular structure modeling tool that integrates cryo-EM density information with a diffusion-model-based structure prediction pipeline.
More here: https://github.com/kiharalab/CryoZeta
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Community Announcement: Upcoming event from our partners at Instruct-ERIC
Instruct Course on Calorimetric and Spectroscopic Characterization of Biomolecules
Sept 7-11, 2026 | Brno, Czechia
Organized in collaboration with Anamet and SpecionRegister here: https://www.ceitec.eu/instruct-course-on-calorimetric-and-spectroscopic-characterization-of-biomolecules/a5545
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Technical Notes: June's software push includes updates to 15 titles -- AlphaFold3, AlphaPulldown, ChemEx, cryoDRGN, DeepDeWedge, EMReady2, OpenForceField Toolkit, MassiveFold, ModelAngelo, PRODIGY, PowerFit, protein-quest, Scipion, STOPGAP, and TOMOMAN.
More here: https://sbgrid.org/software/recent/archive/2026/06/
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SBGrid's eLife paper received a citation in June from Craig Bingman from University of Wisconsin-Madison, in Journal of Agricultural and Food Chemistry: Oxidative Characteristics of Turkey Hemoglobin A Containing Covalently Bound Epigallocatechin Gallate.
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Meharry Medical College student Mudiare Ikoba highlights a publication from SBGrid member Alexandra Trkola and colleagues at the University of Zurich in which the authors propose including people living with HIV in vaccination trials to gain a deeper understanding of the immunologic response to broadly neutralizing antibody-based HIV vaccines.
Read more here: https://medium.com/sbgrid-community-news/could-treatment-inform-prevention-bnab-based-vaccines-for-people-living-with-hiv-ef8b6caf7ceb
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Join us July 14th for the last in this season's software webinars with a presentation on the cryo-ET tools Ais and Pom from Mart So-Last of the Allegretti group at MRC Laboratory of Molecular Biology (LMB).
Tues, July 14, 2026 - 12:00pm ET
Ais and PomRegister here: https://sbgrid.org/webinars/
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Fisk University student Cariuna Ellison's highlight features a publication from the laboratories of Douglas Reese and Bill Clemons of Caltech that describe the cryo-EM structure of a bacterial metalloid pump and the mechanisms that could offer more insight into ridding environments of toxic metalloids.
Read more here: https://medium.com/sbgrid-community-news/kicking-arsenic-to-the-curb-9f6571268e03
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New Title Alert: CryoROLE- is a python package designed to analyze the particle distribution of the relative orientation between two independently refined domains of a biological complex.
More here: https://github.com/yifancheng-ucsf/cryorole
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New Title Alert: Germinal- is a pipeline for designing de novo antibodies against specified epitopes on target proteins. The pipeline follows a 3-step process: hallucination based on ColabDesign, selective sequence redesign with AbMPNN, and cofolding with a structure prediction model.
More here: https://github.com/SantiagoMille/germinal
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SBGrid's eLife paper received a citation in May from Dirk Slotboom from University of Groningen in Journal of Biological Chemistry: NAAC: An affinity chromatography strategy enabling characterization and quantification of influenza.
Read more more: https://doi.org/10.1016/j.jbc.2026.113138
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Community Announcements:
Upcoming event from our partners at Instruct-ERIC
Instruct-ERIC hands-on workshop on: Advanced cryo-FIB-SEM methods
Nov 9-13, 2026 | Heidelberg, Germany
Organized by the EMBL Imaging Centre -
New Title Alert: miss-alignment- is a GPU-based tool for improving cryo-ET tilt-series alignments, designed to run from an initial eTomo/WarpTools patch-tracking alignment.
More here: https://github.com/warpem/miss-alignment/
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SBGrid's eLife paper received a citation in May from Lynne Howell at University of Toronto in Journal of Biological Chemistry: Bacillus cereus PelADA is a polysaccharide de-N-acetylase required for Pel-dependent biofilm formation.
Read more here: https://buff.ly/851Xyt2
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SBGrid's eLife paper received a citation in May from K. Christopher Garcia at Stanford University School of Medicine in Nature Biotechnology: Deep peptide recognition profiling decodes TCR specificity and enables disease-associated antigen discovery.
Read more here: https://doi.org/10.1038/s41587-026-03128-x
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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: https://github.com/IsoNet-cryoET/IsoNet2
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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: https://github.com/swing-research/CryoLithe
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Greetings and an #introduction from the #SBGrid team. We curate and install 500-ish #structuralbiology applications (#CryoEM, #crystallograpy, #NMR, #tomography), host educational #webinars, support #reproducibility, validation, and reprocessing of data, and help scientists get access to the latest tools to get the job done.