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sbgrid.bsky.social
SBGrid Consortium
@sbgrid.bsky.social
1.5K followers 190 following 410 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
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.
buff.ly
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.
buff.ly
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.

Read more here: buff.ly/UNLUraF

#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.

Read more here: buff.ly/2K3e0dk

#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…
buff.ly
November 6, 2025 at 5:03 PM
sbgrid.bsky.social
SBGrid's eLife paper received a citation in October from@sshaolab.bsky.social from @harvardmed.bsky.social in @science.org : GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling.

Read more here: buff.ly/maTT8Ih

#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…
buff.ly
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.
buff.ly
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
buff.ly
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.

Read more here: buff.ly/XZU9yvR

#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…
buff.ly
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!

Read more here: buff.ly/X2JvvSm

#SBGridMemberNews
National Academy of Medicine Elects 8 HMS Faculty to Class of 2025
Recognized for major contributions to improving health for everyone, everywhere
buff.ly
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...
buff.ly
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.

Read more here: buff.ly/xqvFJ8g

#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…
buff.ly
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.…
buff.ly
October 27, 2025 at 4:07 PM
sbgrid.bsky.social
New Member Alert: Cristina Vega from Margarita Salas Center for Biological Research joined SBGrid in September. Welcome!
October 24, 2025 at 4:45 PM
sbgrid.bsky.social
New Title Alert: HADDOCK3- is the next generation integrative modeling software in the long-lasting HADDOCK project.

Learn more here: buff.ly/gInH6VV

#SBGrid #SBGridSoftware #StructuralBiology
A brief introduction to HADDOCK3 — haddock3 3.0.0 documentation
HADDOCK3 is the next generation integrative modelling software in the long-lasting HADDOCK project. It represents a complete rethinking and rewriting of the HADDOCK2.X series, implementing a new way…
buff.ly
October 24, 2025 at 4:08 PM
sbgrid.bsky.social
SBGrid's eLife paper received a citation in September from M. Gordon Joyce from the Walter Reed Army Institute of Research in mBio.

Read more here: buff.ly/nlGJ59X

#SBGrid #StayConnected
First-generation N-terminal domain supersite public antibodies retain activity against Omicron-derived lineages and protect mice against Omicron BA.5 challenge | mBio
As SARS-CoV-2 circulating variants evolve, it is important to understand the vulnerabilities of these viruses to neutralizing antibodies. Within this manuscript, we describe first-generation…
buff.ly
October 23, 2025 at 4:07 PM
sbgrid.bsky.social
SBGrid's eLife paper received a citation in September from Ji-Joon Song from Korea Advanced Institute of Science and Technology in @cp-molcell.bsky.social.

Read more here: buff.ly/XR4zh3Q

#SBGrid #ScienceMatters
Structural determinants of DANGEROUS MIX 3, an alpha/beta hydrolase that triggers NLR-mediated genetic incompatibility in plants
Wan, Kim, et al. provide cryo-EM structures of DANGEROUS MIX 3 (DM3) metabolic enzyme complexes from two Arabidopsis natural accessions, revealing an immune switch. Compromised DM3 dimer interface…
buff.ly
October 22, 2025 at 5:05 PM
sbgrid.bsky.social
New Title Alert: DockQ- a quality measure for protein, nucleic acid, and small molecule docking models that provides a single continuous scoring metric.

Learn more here: buff.ly/YjzUhgo

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - wallnerlab/DockQ: DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models
DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models - wallnerlab/DockQ
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October 22, 2025 at 4:07 PM
sbgrid.bsky.social
SBGrid's eLife paper received a citation in September from Eric Fischer from @danafarber.bsky.social in @natcomms.nature.com Structural basis of VCP-VCPIP1-p47 ternary complex in Golgi maintenance.

Read more here: buff.ly/4xm6yI1

#SBGrid #ScienceMatters
Structural basis of VCP-VCPIP1-p47 ternary complex in Golgi maintenance - Nature Communications
VCPIP1 is a deubiquitylase that binds the essential protein VCP/p97. Here, the authors present cryo-EM structures of VCPIP1 bound to VCP and the VCP-VCPIP1-p47 ternary complex along with biochemical…
buff.ly
October 21, 2025 at 4:06 PM
sbgrid.bsky.social
New Member Alert: @wenyili68.bsky.social from La Trobe University joined SBGrid in September. Welcome!
October 20, 2025 at 5:31 PM
sbgrid.bsky.social
New Title Alert: DeepRank-GNN-esm- a graph neural network framework for scoring protein-protein interfaces that incorporates ESM-2 language model embeddings.

Learn more here: buff.ly/yVPMBTz

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - haddocking/deeprank-gnn-esm: Graph Network for protein-protein interface including language model features
Graph Network for protein-protein interface including language model features - haddocking/deeprank-gnn-esm
buff.ly
October 20, 2025 at 4:20 PM
sbgrid.bsky.social
New Title Alert: TomoStarPy- a collection of Python scripts for manipulating Relion tomo STAR files and performing various cryo-electron tomography data processing tasks.

Learn more here: buff.ly/wta0zXt

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - fuzikt/tomostarpy: Python scripts to manipulate Relion tomo STAR files and much more...
Python scripts to manipulate Relion tomo STAR files and much more... - fuzikt/tomostarpy
buff.ly
October 17, 2025 at 4:07 PM
sbgrid.bsky.social
New Title Alert: cryoTIGER- (Tilt Interpolation Generator for Enhanced Reconstruction) in cryo-electron tomographya computational workflow leveraging a deep learning-based frame interpolation to generate intermediate tilt images.

Learn more here: buff.ly/j7S8zMZ

#SBGrid #SBGridSoftware
October 17, 2025 at 3:45 PM