SBGrid Consortium

Mapping bacteriophages SBGrid member Mihnea Bostina helps to uncover the first high-resolution, head-to-tail structural map of a Felixounavirus bacteriophage.

Mapping bacteriophages: a publication highlight from @keandreyam.bsky.social featuring a new article from the lab of Mihnea Bostina at the @universityofotago.bsky.social & colleagues.

Read more here: buff.ly/Wgfu3bt

#SBGrid #cryoem

Reshaping membranes Melanie Ohi from the University of Michigan studies membrane proteins that work together as complex molecular machines.

Melanie Ohi from @umich.edu is the focus of our November member tale. Ohi stuck with cryoEM, despite warnings that becoming a "blobologist" would limit her options.

Read more here: buff.ly/nPzs4rm

#SBGridTales #Stayconnected

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.… TomoNet

For our November software webinar we heard from Hui Wang from UCLA on TomoNet - Automatic Particle Picking of Flexible Lattice-Like Structures for CryoET.

If you missed it, you can watch it on SBGrid's YouTube channel:

buff.ly/gnhR2AV

#SBGrid #Webinars

COOT Update: We have added a stand-alone versions of & Coot for Linux and for ARM & Intel-based Macs that are available for academic, non-profit, commercial members to download. These versions will work with MacOS Tahoe & are not dependent on other applications.

#SBGrid #SoftwareUpdates

Technical Notes: MacOS 26 Tahoe issues--We recommend that users hold off upgrading to MacOS Tahoe since XQuartz-based OpenGL acceleration is partly broken. These issues impact software that rely on XQuartz, such as Coot.

#SBGrid #SoftwareUpdates

Functional and Structural Studies on the Esperamicin Thioesterase and Progress toward Understanding Enediyne Core Biosynthesis Enediynes are among the most potent antitumor and antibacterial natural products. Studies on their biosynthetic pathways have identified a shared, linear polyene precursor generated from an iterative…

SBGrid's eLife paper received a citation in October from George Phillips Jr. in Journal of Natural Products: Functional and Structural Studies on the Esperamicin Thioesterase and Progress toward Understanding Enediyne Core Biosynthesis.

Read more here: buff.ly/Exh9hxZ

#SBGrid #ScienceMatters

GitHub - bionanopatterning/Pom: Scaling data analyses in cellular cryoET using comprehensive segmentation. Scaling data analyses in cellular cryoET using comprehensive segmentation. - bionanopatterning/Pom

New Title Alert: Pom- a tool for scaling data analyses in cellular cryoET using comprehensive segmentation.

Learn more here: buff.ly/qisPeYQ

#SBGrid #SBGridSoftware #StructuralBiology

Cryo-EM structure of endogenous Pfs230:Pfs48/45 complex with six antibodies reveals mechanisms of malaria transmission-blocking activity The Pfs230:Pfs48/45 complex is the target of leading anti-malaria transmission-blocking vaccine candidates, yet its molecular assembly is poorly understood. Bekkering, Yoo, Hailemariam, et al.…

SBGrid's eLife paper received a citation in October from Jean-Philippe Julien from @sickkidsto.bsky.social Research Institute in Immunity.

Read more here: buff.ly/aXP3Rl3

#SBGrid #StructuralBiology

Molecular Modeling Software | OpenEye Scientific Molecular modeling and cheminformatics software tools built in the cloud to accelerate lead discovery and optimization in drug development.

New Title Alert: OpenEye Academic Package- tools to help design potent and selective bioactive molecules.

Learn more here: buff.ly/SMacQQa

#SBGrid #SBGridSoftware #StructuralBiology

LARGE1 processively polymerizes length-controlled matriglycan on prodystroglycan - Nature Communications LARGE1 glycosyltransferase synthesizes matriglycan (xylose-glucuronate)n on dystroglycan, and short matriglycan can cause neuromuscular disorders. Authors show that LARGE1 processively polymerizes…

SBGrid's eLife paper received a citation in October from Kevin Campbell from University of Iowa in Nature Magazine: LARGE1 processively polymerizes length-controlled matriglycan on prodystroglycan.

Read more here: buff.ly/wg8IVnm

#SBGrid #StayConnected

New Title Alert: nvMolKit- is a CUDA-backed Python library for accelerating common RDKit molecular operations through batch-oriented GPU processing.

Learn more here: buff.ly/pqV1HiF

#SBGrid #SBGridSoftware #StructuralBiology

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…

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.
Read more here: buff.ly/PEtyyKk

#SBGrid

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

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

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.

SBGrid's eLife paper received a citation in October from@gogo-science.bsky.social from Icahn School of Medicine at Mount Sinai in @science.org Immunology.

Read more here: buff.ly/s8uVL86

#SBGrid #ScienceMatters #StayConnected

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 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

GitHub - apple/ml-simplefold Contribute to apple/ml-simplefold development by creating an account on GitHub.

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

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: 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.

More here: buff.ly/uLpQznY

#SBGridSoftware #SBGridUpdates

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

GitHub - yehlincho/BoltzDesign1 Contribute to yehlincho/BoltzDesign1 development by creating an account on GitHub.

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

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…

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

Read more here: buff.ly/WpLjDy6

#SBGrid #StayConnected

GitHub - oxpig/ANARCI: Antibody Numbering and Antigen Receptor ClassIfication Antibody Numbering and Antigen Receptor ClassIfication - oxpig/ANARCI

New Title AlertL: ANARCI- Antibody Numbering and Antigen Receptor ClassIfication.

Learn more here: buff.ly/i8FmJQx

#SBGrid #SBGridSoftware #StructuralBiology

GitHub - alisiafadini/ROCKET Contribute to alisiafadini/ROCKET development by creating an account on GitHub.

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

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.

GitHub - uw-ipd/RoseTTAFold2 Contribute to uw-ipd/RoseTTAFold2 development by creating an account on GitHub.

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

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.

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

Out-competing COVID This publication highlight is part of the SBGrid Communities Project focused on science education and demonstrating how structural biology…

@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

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…

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

GitHub - bionanopatterning/Ais Contribute to bionanopatterning/Ais development by creating an account on GitHub.

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

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.… ROCKET

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

GitHub - anmartinezs/polnet: Generates synthetic datasets for Cryo-Electron Tomography Generates synthetic datasets for Cryo-Electron Tomography - anmartinezs/polnet

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