New Member Alert: Eddy Arnold from @rutgersu.bsky.social joined SBGrid in March. Welcome!!

GitHub - wieczoreklab/MiCSPARC: Microtubule Image Processing in CryoSPARC Pipeline Microtubule Image Processing in CryoSPARC Pipeline - wieczoreklab/MiCSPARC

New Title Alert: MiCSPARC- is a CryoSPARC-based cryo-EM pipeline for microtubule image processing that combines automated filament tracing, particle picking, fast 3D refinement, protofilament-number assignment, alignment, register correction, & seam search.

Learn more here: buff.ly/f1Jmkqe

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Discovery of BBO-11818, a Potent and Selective Noncovalent Inhibitor of (ON) and (OFF) KRAS with Activity against Multiple Oncogenic Mutants The pan-KRAS inhibitor BBO-11818 targets multiple oncogenic KRAS mutants in both active and inactive states, demonstrating strong biochemical, cellular, and in vivo antitumor activity.

SBGrid's eLife paper received a citation in March from Dhirendra Simanshu and Anna Maciag from the Frederick National Laboratory for Cancer Research in Cancer Discovery.

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SegSelect - napari Plugin - Benedikt Wimmer Select a connected component from a membrain-seg segmentation.

New Title Alert: Napari-SegSelect- is a plugin for Napari to select a connected component from a Membrain-seg segmentation.

Learn more here: buff.ly/q1RPNud

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New Member Alert: In March Mamuka Kvaratskhelia from @cuanschutz.bsky.social joined SBGrid. Welcome!!

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 our software webinar on April 14th to hear from José Luis Vilas Prieto on Image processing made simple with scipionTomo.

Tues, April 14, 2026-12:00pm ET
Jose Luis Vilas, Ph.D.
Investigator, National Biotechnology Center, CSIC

Register here: buff.ly/WBjGXUF

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CellArchLab/MemBrain-v2 This is the main repository for MemBrain v2. It includes MemBrain-seg, MemBrain-pick, MemBrain-stats, and several Napari tools. - CellArchLab/MemBrain-v2

New Title Alert: MemBrain-v2- is a tool that includes MemBrain-seg, MemBrain-pick, MemBrain-stats, and several Napari tools.

Learn more here: buff.ly/U3s12Ic

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SBGrid updated the wiki to include guidance for new & existing users. Our revised installation instructions provide clearer instructions for setting up SBGrid buff.ly/5QhSXOR

Expanded Using SBGrid documentation provides more detailed guidance on working w/in the SBGrid environment: buff.ly/rs7dV0l

GitHub - GBLille/AFmassive: AlphaFold version that is extended to integrate diversity parameters for massive sampling. AlphaFold version that is extended to integrate diversity parameters for massive sampling. - GBLille/AFmassive

New Title Alert: AFmassive- is a modified AlphaFold implementation for massive conformational sampling, derived from AlphaFold v2.3.2 and designed to integrate with MassiveFold for parallelized prediction workflows.

Learn more here: buff.ly/jPxTEV0

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Overcoming T cell tolerance to tumor self-antigens through catch-bond engineering T cells are often weakly responsive to tumor self-antigens because of central tolerance, constraining their ability to eliminate tumors. We exploited mechanical force to engineer a weakly reactive T…

SBGrid's eLife paper received a citation in March from K. Christopher Garcia from @stanford.edu School of Medicine in @science.org: Overcoming T cell tolerance to tumor self-antigens through catch-bond engineering.

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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: March's software push includes updates to AlphaPulldown, AreTomo, Coot, CCP4, CryoLithe, DIALS, Doppio, Java, MPicker, OpenFreeEenergy, Open Force Field, qfit, SAMtools, Schrodinger, Scipion, and Xmipp.

More here: buff.ly/WXLwT6q

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PXDesign — De Novo Design of Protein Binders PXDesign: Fast, Modular, and Accurate — De Novo Design of Protein Binders

New Title Alert: PXDesign- is a de novo protein-binder design suite combining a diffusion generator (PXDesign-d) with Protenix and AF2-IG confidence models for candidate selection and ranking.

Learn more here: buff.ly/s455Ck8

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Structure-guided Antibiotics Andrés Palencia of National Institute of Health and Medical Reserves works to develop drugs to combat drug-resistant bacteria and…

Our member tale for March features @palencialab.bsky.social from @inserm.fr in Grenoble, France where his group is harnessing the matchmaking qualities of the LeuRS enzyme in efforts to advance a new class of drugs to tackle drug-resistant bacteria & parasites.

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SBGrid's eLife paper received a citation in February from @cryoet.bsky.social from @jhu.edu School of Medicine and Dylan Hale (now at University of Pittsburgh) in @natcomms.nature.com.

Read more here: buff.ly/kx5Fiaw

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Nucleotide signals coordinate activation and inhibition of bacterial immunity - Nature Biochemical and structural studies show that the bacterial dGTPase CloA is activated by virally produced dTTP and inhibited by 5′-triphosphothymidyl-3′5′-thymidine produced by its regulatory partner…

SBGrid's eLife paper received a citation in February from Philip Kranzusch from @danafarber.bsky.social in @Nature: Nucleotide signals coordinate activation and inhibition of bacterial immunity.

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Conformational ensembles of the magnesium channel CorA reveal structural basis for channel gating | PNAS In prokaryotes, CorA is the primary influx pathway for magnesium, a critical divalent cation in cellular physiology and biochemistry. Mechanistic s...

SBGrid's eLife paper received a citation in February from Anthony Kossiakoff from The University of Chicago in @pnas.org : Conformational ensembles of the magnesium channel CorA reveal structural basis for channel gating.

Read more here: buff.ly/3Oawrum

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GitHub - vosslab/vossvolvox: This repository provides C++17 command-line tools for analyzing molecular structures by computing volumes, channels, cavities, and tunnel geometry from PDB, mmCIF, PDBML, or XYZR inputs. It is intended for researchers in structural biology and molecular biophysics who need reproducible grid-based analyses. This repository provides C++17 command-line tools for analyzing molecular structures by computing volumes, channels, cavities, and tunnel geometry from PDB, mmCIF, PDBML, or XYZR inputs. It is inte...

New Title Alert: vossvolvox- a C++17 command-line tools for analyzing molecular structures, specifically for computing volumes, channels, cavities, and tunnel geometry from various molecular input formats.

Learn more here: buff.ly/0ff33pF

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Bacterial immune activation via supramolecular assembly with phage triggers - Nature An antiphage defence system has an activation mechanism that relies on the sensing of phage-encoded proteins that enforce geometry crucial to activation and are not typically present in non-infected…

SBGrid's eLife paper received a citation in February from Alireza Ghanbarpour from Washington University School of Medicine in St. Louis, in @Nature: Bacterial immune activation via supramolecular assembly with phage triggers.

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Technical Notes:

Phenix 2 / Coot 1 integration update: The Phenix/Coot GUI integration is not currently working; the Phenix developers are targeting a fix for their next official release.

SBGrid's eLife paper received a citation in February from Christopher Garcia from @stanforduniversity.bsky.social School of Medicine in @science.org: Structural ontogeny of protein-protein interactions.

Read more here: buff.ly/BPRhfUL

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SBGrid's eLife paper received a citation in February from Eric Fischer from @danafarber.bsky.social in @natchembio.nature.com

High-throughput ligand diversification to discover chemical inducers of proximity.

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We've published some initial documentation on using individual or group SBGrid installations on HPC resources where creating a `/programs/` link is problematic. Please contact us at accounts@sbgrid.org if you encounter problems.

Learn more here:

Open Force Field 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.…

In case you missed Joshua Mitchell webinar featuring Open Force Field Initiative, it is now available in our YouTube channel.

More here: buff.ly/6tzRrM8

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Hope for hard-to-treat heart disease A discovery in a Harvard lab is offering hope for patients with a type of heart disease with few approved therapies and high mortality rates.

Member News: SBGrid member Andrew Kruse, professor of biological chemistry & molecular pharmacology in the Blavatnik Institute at HMS is featured in The Harvard Gazette for his discovery offering hope for patients with hard-to-treat heart disease.

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Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET - Nature Protocols A protocol for cryogenic 3D correlative focused ion beam milling using an integrated fluorescence light microscope and montage cryo-ET for nonadherent and adherent mammalian cells, as well as primary…

SBGrid's eLife paper received a citation in February from Elizabeth Wright from @uwmadison.bsky.social in @natprot.nature.com : Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET.

Read more here: buff.ly/EGZomRA

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GitHub - manifoldbio/mber-open: mBER - Manifold Binder Engineering and Refinement. mBER enables antibody binder design by leveraging structure templates and sequence conditioning in backprop design through AlphaFold-Multimer. Preprint: https://www.biorxiv.org/content/10.1101/2025.09.26.678877v1 mBER - Manifold Binder Engineering and Refinement. mBER enables antibody binder design by leveraging structure templates and sequence conditioning in backprop design through AlphaFold-Multimer. Pre...

New Title Alert: mBER-open- is a protein design framework for antibody binder design that leverages structure templates and sequence conditioning in backpropagation-based design through AlphaFold-Multimer.

Learn more here: buff.ly/59LkTAm

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A postdoc fellowship & postbac position are available in the Cell Biology & Biophysics Unit headed by Dr. Antonina Roll-Mecak.

Please send your CV, research experience summary & contact info of three references to Antonina@nih.gov Please write “Tubulin code” in the subject header.

SBGrid's eLife paper received a citation in February from James Berger from @jhu.edu School of Medicine in @natcomms.nature.com : Supercoiled DNA recognition and cleavage control in topoisomerase VI.

Read more here: buff.ly/tKmGHHK

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SBGrid's eLife paper received a citation in February from John Pascal from Université de Montréal (University of Montreal) in @natcomms.nature.com : PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation.

Read more here: buff.ly/VbygZD2

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New Member Alert: Dylan Hale from University of Pittsburgh joined SBGrid in February. Welcome!!