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sbgrid.bsky.social
SBGrid Consortium
@sbgrid.bsky.social
1.5K followers 190 following 420 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.bsky.social
SBGrid's eLife paper received a citation from a review in @natrevmethodsprimers.nature.com. Contributions from member labs & contributing developers, including Pavel Afonine, Kay Diederichs, Eugene Krissinel, Jose Antonio Marquez, Andrea Thorn & Isabel Usón.
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#SBGrid
Macromolecular crystallography - Nature Reviews Methods Primers
This Primer offers a practical and rational introduction to macromolecular crystallography, whether to engage directly with or to critically assess results, with a focus on understanding the…
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November 20, 2025 at 5:03 PM
sbgrid.bsky.social
New Title Alert: Icecream- a self-supervised framework for cryo-ET reconstruction that integrates equivariance principles from modern imaging theory into a deep-learning architecture.

Learn more here: buff.ly/bdepEUm

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - swing-research/icecream: 🍦Icecream: a self-supervised framework for cryo-ET reconstruction
🍦Icecream: a self-supervised framework for cryo-ET reconstruction - swing-research/icecream
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November 19, 2025 at 5:03 PM
sbgrid.bsky.social
SBGrid's eLife paper received a citation in October [email protected] from Icahn School of Medicine at Mount Sinai in @science.org Immunology.

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#SBGrid #ScienceMatters #StayConnected
Germinal center–mediated broadening of B cell responses to SARS-CoV-2 booster immunization
SARS-CoV-2 variant booster vaccination broadens human B cell responses through the germinal center reaction.
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November 18, 2025 at 5:05 PM
sbgrid.bsky.social
Join us November 18th to hear from Hui Wang, postdoc in the Hong Zhou lab at @uofcalifornia.bsky.social, Los Angeles, on TomoNet: Automatic Particle Picking of Flexible Lattice-Like Structures for CryoET.

Register here: buff.ly/QAMUkym

#SBGrid #StructuralBiology #Webinars
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…
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November 17, 2025 at 5:05 PM
sbgrid.bsky.social
New Title Alert: SimpleFold- is the first flow-matching based protein folding model that uses only general purpose transformer layers, without relying on expensive modules like triangle attention or pair representation biases.

Learn more here: buff.ly/bfv8nwT

#SBGrid #SBGridSoftware
GitHub - apple/ml-simplefold
Contribute to apple/ml-simplefold development by creating an account on GitHub.
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November 17, 2025 at 1:58 AM
sbgrid.bsky.social
Technical Notes: October's software push includes updates to ChimeraX, DeepRank-GNN-ESM, MDAnalysis, NGLView, NmrPipe, Open Force Field Toolkit, Open Free Energy, PowerFit, PyTOM-match-pick, RDKit, and TomoNet.

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#SBGridSoftware #SBGridUpdates
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…
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November 14, 2025 at 5:04 PM
sbgrid.bsky.social
New Title Alert: CTFMeasure- a software for estimating CTF parameters of cryo-ET tilt series. It features tilt-series-based joint estimation and Thon ring rescaling technique.

Learn more here: buff.ly/zh57gUB

#SBGrid #SBGridSoftware #StructuralBiology
CTFMeasure · Xueming Li Lab
CTFMeasure is a software for estimating CTF parameters of cryo-ET tilt series. It features tilt-series-based joint estimation and Thon ring rescaling technique to retrieve power spectrums with higher…
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November 13, 2025 at 5:04 PM
sbgrid.bsky.social
New Title Alert: BoltzDesign- is a molecular design tool powered by the Boltz model for designing protein-protein interactions and biomolecular complexes.

Learn more here: buff.ly/P9BTlAZ

#SBGridSoftware #SBGrid
GitHub - yehlincho/BoltzDesign1
Contribute to yehlincho/BoltzDesign1 development by creating an account on GitHub.
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November 12, 2025 at 6:03 PM
sbgrid.bsky.social
SBGrid's eLife paper received a citation in October from Halil Aydin from @nyu.edu and Matteo Dal Peraro from @lbm-epfl.bsky.social , EPFL Lausanne in @natcomms.nature.com

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#SBGrid #StayConnected
Cardiolipin dynamics promote membrane remodeling by mitochondrial OPA1 - Nature Communications
This study reveals how cardiolipin governs mitochondrial morphology by modulating the activity of human OPA1 and how its replacement by monolyso-cardiolipin, as observed in Barth syndrome, impacts…
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November 12, 2025 at 5:04 PM
sbgrid.bsky.social
New Title AlertL: ANARCI- Antibody Numbering and Antigen Receptor ClassIfication.

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#SBGrid #SBGridSoftware #StructuralBiology
GitHub - oxpig/ANARCI: Antibody Numbering and Antigen Receptor ClassIfication
Antibody Numbering and Antigen Receptor ClassIfication - oxpig/ANARCI
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November 11, 2025 at 5:04 PM
sbgrid.bsky.social
New Title Alert: ROCKET- is a tool for refining AlphaFold predictions using crystallographic and cryo-EM likelihood targets.

Learn more here: buff.ly/s9y4bFV

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - alisiafadini/ROCKET
Contribute to alisiafadini/ROCKET development by creating an account on GitHub.
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November 10, 2025 at 5:30 PM
sbgrid.bsky.social
Technical Notes from our Software Team:

Coot issues in MacOS Tahoe: A reminder to Coot users that we recommend waiting to upgrade to the latest macOS (Tahoe) due to problems with XQuartz-based OpenGL acceleration. We are monitoring the issue and will provide updates when available.
November 10, 2025 at 5:08 PM
sbgrid.bsky.social
New Title Alert: RoseTTAFold2- a tool that extends the original three-track architecture of RoseTTAFold over the full network.

Learn more here: buff.ly/wQ22ZM2

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - uw-ipd/RoseTTAFold2
Contribute to uw-ipd/RoseTTAFold2 development by creating an account on GitHub.
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November 7, 2025 at 5:31 PM
sbgrid.bsky.social
How one protein tail helps starve bacteria of zinc: a publication highlight chosen by recent Ph.D. graduate @keandreyam.bsky.social , Ph.D. (congratulations KeAndreya!) from the laboratory of @chazinwalter.bsky.social to highlight.

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#SBGrid #Calprotectin
Left: Structure of the S100A8 (magenta)/S100A9 (cyan) heterodimer of calprotectin bound to zinc ion (sphere). Right: Close-up of the histidine residues (orange) coordinating zinc ion. PDB ID 8SJC. CC BY SBGRID.
November 7, 2025 at 5:05 PM
sbgrid.bsky.social
@caltech.edu doctoral student Vida Robertson highlighted a publication from John Williams of @cityofhope.bsky.social and colleagues, who developed a new coronavirus biologic that tightly binds to SARS-CoV-2 spike proteins.

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#SBGrid #CryoEM #COVID-19
Out-competing COVID
This publication highlight is part of the SBGrid Communities Project focused on science education and demonstrating how structural biology…
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November 6, 2025 at 5:03 PM
sbgrid.bsky.social
SBGrid's eLife paper received a citation in October [email protected] from @harvardmed.bsky.social in @science.org : GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling.

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#SBGrid #StayConnected #ScienceMatters
GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling
During nutrient deprivation, activation of the protein kinase GCN2 regulates cell survival and metabolic homeostasis. In addition to amino acid stress, GCN2 is activated by a variety of cellular…
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November 5, 2025 at 6:01 PM
sbgrid.bsky.social
New Title Alert: Ais- a tool that provides annotation and segmentation of cryo-ET data using convolutional neural networks.

Learn more here: buff.ly/29QIm9Q

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - bionanopatterning/Ais
Contribute to bionanopatterning/Ais development by creating an account on GitHub.
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November 5, 2025 at 5:01 PM
sbgrid.bsky.social
If you missed the live presentation with
@alisiafadini.bsky.social and @minhuanli.bsky.social introducing ROCKET, you can watch the video on SBGrid's YouTube channel.

More here: buff.ly/nsA12eg

#SBGrid #Webinars
ROCKET
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.…
youtu.be
November 4, 2025 at 5:02 PM
sbgrid.bsky.social
New Title Alert: PolNet- a Python package for generating synthetic datasets of the cellular context for Cryo-Electron Tomography.

Learn more here: buff.ly/MEUzeIi

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - anmartinezs/polnet: Generates synthetic datasets for Cryo-Electron Tomography
Generates synthetic datasets for Cryo-Electron Tomography - anmartinezs/polnet
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October 31, 2025 at 4:05 PM
sbgrid.bsky.social
SBGrid's eLife paper received a citation in September from Dhirendra Simanshu from Frederick National Laboratory for Cancer Research in Science: Structural basis for LZTR1 recognition of RAS GTPases for degradation.

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#SBGrid #StayConnected
Structural basis for LZTR1 recognition of RAS GTPases for degradation
The RAS family of small guanosine triphosphatases (GTPases) are tightly regulated signaling molecules that are further modulated by ubiquitination and proteolysis. Leucine Zipper-like Transcription…
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October 30, 2025 at 4:06 PM
sbgrid.bsky.social
New Member Alert: Susanne Kassube & @weiss-lab.bsky.social from the University of Zurich joined SBGrid in September. Welcome!!
October 29, 2025 at 5:06 PM
sbgrid.bsky.social
SBGrid Member Sun Hur was elected to the National Academy of Medicine. Congratulations!

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#SBGridMemberNews
National Academy of Medicine Elects 8 HMS Faculty to Class of 2025
Recognized for major contributions to improving health for everyone, everywhere
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October 29, 2025 at 5:04 PM
sbgrid.bsky.social
New Title Alert: OpenForceField Toolkit- a Python toolkit for the development and application of modern molecular mechanics force fields, leveraging direct chemical perception and rigorous statistical parameterization methods.

Learn more here: buff.ly/yUSrikn

#SBGrid #SBGridSoftware
GitHub - openforcefield/openff-toolkit: The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io - ope...
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October 29, 2025 at 4:07 PM
sbgrid.bsky.social
SBGrid's eLife paper received a citation in September from @jpglmrodrigues.bsky.social from Schrödinger, Inc. in FEBS Letters: Towards better structural models from cryo-electron microscopy data with physics-based methods.

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#SBGrid #ScienceMatters
Towards better structural models from cryo-electron microscopy data with physics-based methods - PubMed
Cryo-electron microscopy can now routinely deliver atomic resolution structures for a variety of biological systems. The relevance and value of these structures are directly related to their ability…
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October 28, 2025 at 4:07 PM
sbgrid.bsky.social
New Title Alert: OpenFreeEnergy- is a Python package for executing alchemical free energy calculations.

Learn more here: buff.ly/QcyIk1X

#SBGrid #SBGridSoftware #StructuralBiology
Open Free Energy
Open Free Energy is dedicated to developing software that is not only stable and reliable for industrial needs but also fosters the development of new methods destined to become industry standards.…
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October 27, 2025 at 4:07 PM