#sbgrid — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #sbgrid, aggregated by home.social.
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New Title Alert: CryoBoltz- is a method for fitting atomic structures into cryo-EM density maps of dynamic proteins. It is built on top of Boltz-1, a state-of-the-art structure prediction model for biomolecular complexes.
Learn more here: https://cryoboltz.cs.princeton.edu/
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SBGrid's eLife paper received a citation in April from Antonina Roll-Mecak from the The National Institutes of Health in Nature Structural and Molecular Biology: Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state.
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New Title Alert: AlphaJudge- is a Python pipeline for evaluating AlphaFold2 and AlphaFold3 protein complex predictions by combining model confidence metrics such as ipTM, pTM, pLDDT, and PAE with interface-level biophysical descriptors including contacts, hydrogen bonds, salt bridges, buried area, solvation proxy, and shape complementarity.
Learn more here: https://github.com/KosinskiLab/AlphaJudge
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New Title Alert: AlphaJudge- is a Python pipeline for evaluating AlphaFold2 and AlphaFold3 protein complex predictions by combining model confidence metrics such as ipTM, pTM, pLDDT, and PAE with interface-level biophysical descriptors including contacts, hydrogen bonds, salt bridges, buried area, solvation proxy, and shape complementarity.
Learn more here: https://github.com/KosinskiLab/AlphaJudge
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New Title Alert: AlphaJudge- is a Python pipeline for evaluating AlphaFold2 and AlphaFold3 protein complex predictions by combining model confidence metrics such as ipTM, pTM, pLDDT, and PAE with interface-level biophysical descriptors including contacts, hydrogen bonds, salt bridges, buried area, solvation proxy, and shape complementarity.
Learn more here: https://github.com/KosinskiLab/AlphaJudge
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SBGrid's eLife paper received a citation in April from Dirk Slotboom from University of Groningen in Nature Communications: Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters.
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SBGrid's eLife paper received a citation in April from Dirk Slotboom from University of Groningen in Nature Communications: Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters.
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SBGrid's eLife paper received a citation in April from Dirk Slotboom from University of Groningen in Nature Communications: Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters.
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Technical Notes: April's software push includes updates to twelve titles -AlphaPulldown, Avogadro, BioEmu, ChemEx, ColabFold, CryoAtom, Foldtree, OpenFold3, PyMOL, Relion, Scipion, and TomoNet.
More here: https://sbgrid.org/software/recent/archive/2026/04/
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Technical Notes: April's software push includes updates to twelve titles -AlphaPulldown, Avogadro, BioEmu, ChemEx, ColabFold, CryoAtom, Foldtree, OpenFold3, PyMOL, Relion, Scipion, and TomoNet.
More here: https://sbgrid.org/software/recent/archive/2026/04/
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Technical Notes: April's software push includes updates to twelve titles -AlphaPulldown, Avogadro, BioEmu, ChemEx, ColabFold, CryoAtom, Foldtree, OpenFold3, PyMOL, Relion, Scipion, and TomoNet.
More here: https://sbgrid.org/software/recent/archive/2026/04/
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New Title Alert: af_analysis- is a Python package for analysis of AlphaFold protein structure predictions from AlphaFold 2/3, ColabFold, AlphaFold-Multimer, AlphaPulldown, Boltz1, Chai-1, and MassiveFold.
Learn more here: https://github.com/samuelmurail/af_analysis/
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New Title Alert: af_analysis- is a Python package for analysis of AlphaFold protein structure predictions from AlphaFold 2/3, ColabFold, AlphaFold-Multimer, AlphaPulldown, Boltz1, Chai-1, and MassiveFold.
Learn more here: https://github.com/samuelmurail/af_analysis/
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New Title Alert: af_analysis- is a Python package for analysis of AlphaFold protein structure predictions from AlphaFold 2/3, ColabFold, AlphaFold-Multimer, AlphaPulldown, Boltz1, Chai-1, and MassiveFold.
Learn more here: https://github.com/samuelmurail/af_analysis/
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Join our software webinar on May 12th to hear from Jarrett Johnson, Senior Developer from Schrödinger, on Upcoming improvements to visualization and CryoEM support in PyMOL.
Tuesday, May 12, 2026 - 12:00pm ET
Jarrett Johnson, Ph.D.
Senior Developer, Schrödinger, Inc.Register here: https://sbgrid.org/webinars/
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Join our software webinar on May 12th to hear from Jarrett Johnson, Senior Developer from Schrödinger, on Upcoming improvements to visualization and CryoEM support in PyMOL.
Tuesday, May 12, 2026 - 12:00pm ET
Jarrett Johnson, Ph.D.
Senior Developer, Schrödinger, Inc.Register here: https://sbgrid.org/webinars/
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Join our software webinar on May 12th to hear from Jarrett Johnson, Senior Developer from Schrödinger, on Upcoming improvements to visualization and CryoEM support in PyMOL.
Tuesday, May 12, 2026 - 12:00pm ET
Jarrett Johnson, Ph.D.
Senior Developer, Schrödinger, Inc.Register here: https://sbgrid.org/webinars/
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Community Announcement:
Upcoming event from our partners at Instruc-ERIC
Calorimetric and Spectroscopic Characterization of Biomolecules
September 7-11, 2026 | CEITEC Brno, Czech Republic
Organized in collaboration with the Biomolecular Interactions and Crystallography Core Facility at The Central European Institute of TechnologyRegister here: https://instruct-eric.org/events/instruct-course-on-calorimetric-and-spectroscopic-characterization-of-biomolecules
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Community Announcement:
Upcoming event from our partners at Instruc-ERIC
Calorimetric and Spectroscopic Characterization of Biomolecules
September 7-11, 2026 | CEITEC Brno, Czech Republic
Organized in collaboration with the Biomolecular Interactions and Crystallography Core Facility at The Central European Institute of TechnologyRegister here: https://instruct-eric.org/events/instruct-course-on-calorimetric-and-spectroscopic-characterization-of-biomolecules
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Community Announcement:
Upcoming event from our partners at Instruc-ERIC
Calorimetric and Spectroscopic Characterization of Biomolecules
September 7-11, 2026 | CEITEC Brno, Czech Republic
Organized in collaboration with the Biomolecular Interactions and Crystallography Core Facility at The Central European Institute of TechnologyRegister here: https://instruct-eric.org/events/instruct-course-on-calorimetric-and-spectroscopic-characterization-of-biomolecules
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Meharry Medical College student Mudiare Ikoba highlights a publication in the Journal of Cell Biology from SBGrid member Antonina Roll-Mecak and colleagues in which the authors analyze the structure of the RPGR-TTLL5 complex to shed light on the pathomechanism of retititis pigmentosa.
Read more here: https://medium.com/sbgrid-community-news/how-proteins-work-together-to-support-our-vision-e4e1a30a6850
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Meharry Medical College student Mudiare Ikoba highlights a publication in the Journal of Cell Biology from SBGrid member Antonina Roll-Mecak and colleagues in which the authors analyze the structure of the RPGR-TTLL5 complex to shed light on the pathomechanism of retititis pigmentosa.
Read more here: https://medium.com/sbgrid-community-news/how-proteins-work-together-to-support-our-vision-e4e1a30a6850
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Meharry Medical College student Mudiare Ikoba highlights a publication in the Journal of Cell Biology from SBGrid member Antonina Roll-Mecak and colleagues in which the authors analyze the structure of the RPGR-TTLL5 complex to shed light on the pathomechanism of retititis pigmentosa.
Read more here: https://medium.com/sbgrid-community-news/how-proteins-work-together-to-support-our-vision-e4e1a30a6850
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New Title Alert: AF3Complex- is a model equipped with the same improvements as AF2Complex, along with a novel method for excluding ligands, built on AlphaFold 3.
Learn more here: https://github.com/Jfeldman34/AF3Complex
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New Title Alert: AF3Complex- is a model equipped with the same improvements as AF2Complex, along with a novel method for excluding ligands, built on AlphaFold 3.
Learn more here: https://github.com/Jfeldman34/AF3Complex
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New Title Alert: AF3Complex- is a model equipped with the same improvements as AF2Complex, along with a novel method for excluding ligands, built on AlphaFold 3.
Learn more here: https://github.com/Jfeldman34/AF3Complex
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Fisk University student Cariuna Ellison's highlight features an eLife publication from Jochen Zimmer's group at University of Virginia School of Medicine that describes the use of Cryo-EM to reveal how CvHAS utilizes a two-step mechanism to navigate the balance between substrate specificity and degeneracy.
Read more here: https://medium.com/sbgrid-community-news/molecular-proofreading-mechanisms-of-enzyme-binding-567ed3b5c4f2
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Fisk University student Cariuna Ellison's highlight features an eLife publication from Jochen Zimmer's group at University of Virginia School of Medicine that describes the use of Cryo-EM to reveal how CvHAS utilizes a two-step mechanism to navigate the balance between substrate specificity and degeneracy.
Read more here: https://medium.com/sbgrid-community-news/molecular-proofreading-mechanisms-of-enzyme-binding-567ed3b5c4f2
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Fisk University student Cariuna Ellison's highlight features an eLife publication from Jochen Zimmer's group at University of Virginia School of Medicine that describes the use of Cryo-EM to reveal how CvHAS utilizes a two-step mechanism to navigate the balance between substrate specificity and degeneracy.
Read more here: https://medium.com/sbgrid-community-news/molecular-proofreading-mechanisms-of-enzyme-binding-567ed3b5c4f2
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If you missed our March webinar with José Luis Vilas Prieto on Image processing made simple with ScipionTomo, you can catch up with the recorded version on YouTube.
More here: https://youtu.be/uE8ej9ZO-M8
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If you missed our March webinar with José Luis Vilas Prieto on Image processing made simple with ScipionTomo, you can catch up with the recorded version on YouTube.
More here: https://youtu.be/uE8ej9ZO-M8
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If you missed our March webinar with José Luis Vilas Prieto on Image processing made simple with ScipionTomo, you can catch up with the recorded version on YouTube.
More here: https://youtu.be/uE8ej9ZO-M8
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New Title Alert: PXDesignBench- is a protein design evaluation suite for monomer and binder tasks that standardizes sequence generation, structure consistency assessment, and downstream metrics across tools including ProteinMPNN, ESMFold, AlphaFold2, and Protenix.
Learn more here: https://github.com/bytedance/PXDesignBench
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New Title Alert: PXDesignBench- is a protein design evaluation suite for monomer and binder tasks that standardizes sequence generation, structure consistency assessment, and downstream metrics across tools including ProteinMPNN, ESMFold, AlphaFold2, and Protenix.
Learn more here: https://github.com/bytedance/PXDesignBench
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New Title Alert: PXDesignBench- is a protein design evaluation suite for monomer and binder tasks that standardizes sequence generation, structure consistency assessment, and downstream metrics across tools including ProteinMPNN, ESMFold, AlphaFold2, and Protenix.
Learn more here: https://github.com/bytedance/PXDesignBench
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New Title Alert: MolDiff- is a diffusion framework designed for generating 3D drug-like molecules, achieving a sampling success rate of over 99%. This tool addresses the atom-bond inconsistency problem in 3D molecule diffusion generation and serves as a backbone for applications such as pocket-based generation and linker generation.
Learn more here: https://github.com/pengxingang/MolDiff/
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New Title Alert: MolDiff- is a diffusion framework designed for generating 3D drug-like molecules, achieving a sampling success rate of over 99%. This tool addresses the atom-bond inconsistency problem in 3D molecule diffusion generation and serves as a backbone for applications such as pocket-based generation and linker generation.
Learn more here: https://github.com/pengxingang/MolDiff/
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New Title Alert: MolDiff- is a diffusion framework designed for generating 3D drug-like molecules, achieving a sampling success rate of over 99%. This tool addresses the atom-bond inconsistency problem in 3D molecule diffusion generation and serves as a backbone for applications such as pocket-based generation and linker generation.
Learn more here: https://github.com/pengxingang/MolDiff/
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New Title Alert: Protein-quest- is a Python package to search/retrieve/filter proteins and protein structures.
Learn more here: https://www.bonvinlab.org/protein-quest/
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New Title Alert: Protein-quest- is a Python package to search/retrieve/filter proteins and protein structures.
Learn more here: https://www.bonvinlab.org/protein-quest/
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New Title Alert: Protein-quest- is a Python package to search/retrieve/filter proteins and protein structures.
Learn more here: https://www.bonvinlab.org/protein-quest/
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New Title Alert: MassiveFold- a tool designed to expand structure prediction sampling by optimizing the parallelization of AlphaFold-based predictions across GPU clusters.
Learn more here: https://github.com/GBLille/MassiveFold
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New Title Alert: MassiveFold- a tool designed to expand structure prediction sampling by optimizing the parallelization of AlphaFold-based predictions across GPU clusters.
Learn more here: https://github.com/GBLille/MassiveFold
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New Title Alert: MassiveFold- a tool designed to expand structure prediction sampling by optimizing the parallelization of AlphaFold-based predictions across GPU clusters.
Learn more here: https://github.com/GBLille/MassiveFold
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SBGrid member Stuart Orkin, the Harvard Medical School David G. Nathan Distinguished Professor of Pediatrics at Dana-Farber Cancer Institute and Boston Children's Hospital, has been awarded the 2026 Breakthrough Prize in Life Sciences.
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SBGrid member Stuart Orkin, the Harvard Medical School David G. Nathan Distinguished Professor of Pediatrics at Dana-Farber Cancer Institute and Boston Children's Hospital, has been awarded the 2026 Breakthrough Prize in Life Sciences.
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SBGrid member Stuart Orkin, the Harvard Medical School David G. Nathan Distinguished Professor of Pediatrics at Dana-Farber Cancer Institute and Boston Children's Hospital, has been awarded the 2026 Breakthrough Prize in Life Sciences.
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New Title Alert: MolSnapper- is a tool for conditioning diffusion models to generate 3D drug-like molecules, built on the MolDiff codebase. It integrates pretrained models and provides a streamlined workflow for sampling molecules from defined pockets, making it suitable for structure-based drug design applications.
Learn more here: https://github.com/oxpig/MolSnapper
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New Title Alert: MolSnapper- is a tool for conditioning diffusion models to generate 3D drug-like molecules, built on the MolDiff codebase. It integrates pretrained models and provides a streamlined workflow for sampling molecules from defined pockets, making it suitable for structure-based drug design applications.
Learn more here: https://github.com/oxpig/MolSnapper
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New Title Alert: MolSnapper- is a tool for conditioning diffusion models to generate 3D drug-like molecules, built on the MolDiff codebase. It integrates pretrained models and provides a streamlined workflow for sampling molecules from defined pockets, making it suitable for structure-based drug design applications.
Learn more here: https://github.com/oxpig/MolSnapper