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

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

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

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

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

New Title AlertL: ANARCI- Antibody Numbering and Antigen Receptor ClassIfication. Learn more here: buff.ly/i8FmJQx #SBGrid #SBGridSoftware #StructuralBiology

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.

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

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

@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

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. Read more here: buff.ly/maTT8Ih #SBGrid #StayConnected #ScienceMatters

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

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

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

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

New Member Alert: Susanne Kassube & @weiss-lab.bsky.social from the University of Zurich joined SBGrid in September. Welcome!!

SBGrid Member Sun Hur was elected to the National Academy of Medicine. Congratulations! Read more here: buff.ly/X2JvvSm #SBGridMemberNews

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

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

New Title Alert: OpenFreeEnergy- is a Python package for executing alchemical free energy calculations. Learn more here: buff.ly/QcyIk1X #SBGrid #SBGridSoftware #StructuralBiology

New Member Alert: Cristina Vega from Margarita Salas Center for Biological Research joined SBGrid in September. Welcome!

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

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

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

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

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

New Member Alert: @wenyili68.bsky.social from La Trobe University joined SBGrid in September. Welcome!

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

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

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

SBGrid's eLife paper received a citation in September from Pedro José Barbosa Pereira from Universidade do Porto in Chemical Science Journal. Read more here: buff.ly/H3lVc14 #SBGrid #ScienceMatters

SBGrid's eLife paper received a citation in September from @cryoet.bsky.social from The @jhu.edu School of Medicine in @nature.com : Delta-type glutamate receptors are ligand-gated ion channels. Read more here: buff.ly/0AOhkUx #SBGrid #ScienceMatters

New Title Alert: BindCraft- a user friendly and accurate binder design pipeline. Learn more here: buff.ly/GJJ6wUR #SBGrid #SBGridSoftware #StructuralBiology

On Tuesday, October 14th we are kicking off our software webinar series with @alisiafadini.bsky.social and @minhuanli.bsky.social introducing ROCKET. Register here: buff.ly/J1Ftdr8 #SBGrid #StructuralBiology #Webinars

SBGrid's eLife paper received a citation in September from Jonathan Clinger from @baylor.bsky.social in biomolecules: Multi-Temperature Crystallography of S-Adenosylmethionine Decarboxylase Observes Dynamic Loop Motions. Read more here: buff.ly/qD94vQe #SBGrid #StayConnected

New Member Alert: Pierre Gönczy from École Polytechnique Fédérale de Lausanne joined SBGrid in September. Welcome!!

New Title Alert: ARCTIC-3D- a software for data-mining and clustering of protein interface information. Learn more here: buff.ly/IbbwP2N #SBGridSoftware #StructuralBiology #SBGrid

SBGrid's eLife paper received a citation in September from Jue Chen from @rockefeller.edu in @pnas.org : Structurally diverse viral inhibitors converge on a shared mechanism to stall the antigen transporter TAP. Read more here: buff.ly/HFGbZ9u #SBGrid #ScienceMatters

New Title Alert: prodigy-lig- is a structure-based method for the prediction of binding affinity in protein-small ligand (such as drugs or metabolites) complexes. Learn more here: buff.ly/1PYlZIe #SBGrid #SBGridSoftware #StructuralBiology

September's software push includes updates to- AlphaPulldown, Boltz, ChemEM, ColabDesign, cryoDRGN, EMReady2, GROMACS, HADDOCK, NMRFxAnalyst, NMRFxStructure, PowerFit, PyTom-Match-Pick, R, RDKit, RFDiffusion, Scipion, SSDraw, Starparser, Topaz, Volume_Seg_Tool, & Warp. More here:

Job posting: Research Associate - SBGrid a computationally minded PhD structural biologist interested in advancing research through installing, curating, validating, & benchmarking the software that underpins macromolecular structure determination. academicpositions.harvard.edu/postings/15185

New Member Alert: In September Terje Dokland at the CryoEM Microscopy Facility from University of Alabama at Birmingham joined SBGrid. Welcome!

New Title Alert: AlphaBridge- a script that using the output provided by Alphafold3, provides different plots and files useful for the identification of interacting interfaces. Learn more here: buff.ly/gVZhhhj #SBGrid #SBGridSoftware #StructuralBiology

Getting rid of arsenic: a publication from the lab of William Clemons Jr. from @caltech.edu that reveals how the ArsA enzyme reshapes itself to capture and expel toxic arsenic, providing a structural blueprint for microbial survival. Read more here: buff.ly/OC5nXeF #SBGrid #Arsenic

New Member Alert: @tbeyett.bsky.social at Emory University School of Medicine joined SBGrid in September. Welcome!

@caltech.edu doctoral student Vida Robertson highlighted a publication from Jens Meiler, from @vanderbilt.edu, who describes using Rosetta to design antibiotic peptides called lanthipeptides with antibiotic properties. Read more here: buff.ly/d6k8HvB #SBGrid #NMR #ProteinDesign

New Title Alert: PRODIGY- a collection of web services focused on the prediction of binding affinity in biological complexes as well as the identification of biological interfaces from crystallographic one. Learn more here: buff.ly/mrqcL3V #SBGrid #SBGridSoftware #StructuralBiology

Our member tale for October features Gira Bhabha. Now at @jhu.edu Bhabha's lab is joined w/ Damian Ekiert, her partner in science & in life, where she studies MCE proteins in tuberculosis & the interactions between microsporidia parasites & host cells. Read more here: buff.ly/bz0eCIE #SBGTales