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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
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
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
sbgrid.bsky.social
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
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buff.ly
October 10, 2025 at 4:07 PM
sbgrid.bsky.social
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
GitHub - yehlincho/BoltzDesign1
Contribute to yehlincho/BoltzDesign1 development by creating an account on GitHub.
buff.ly
November 12, 2025 at 6:03 PM
sbgrid.bsky.social
New Title Alert: Foldtree- a snakemake workflow for making and benchmarking structure based trees using Foldseek.

More here: https://github.com/DessimozLab/fold_tree

#SBGrid #structuralbiology #SBGridsoftware
GitHub - DessimozLab/fold_tree: snakemake pipeline for creating trees from sequence sets
snakemake pipeline for creating trees from sequence sets - DessimozLab/fold_tree
github.com
September 13, 2024 at 4:00 PM
sbgrid.bsky.social
New Title Alert: LigandMPNN- a deep learning-based tool for designing protein sequences conditioned on atomic context, including ligands, DNA, RNA, and modified amino acids.

Learn more here: buff.ly/3llSBhI

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - dauparas/LigandMPNN
Contribute to dauparas/LigandMPNN development by creating an account on GitHub.
buff.ly
July 24, 2025 at 4:05 PM
sbgrid.bsky.social
New Title Alert: Vesicle Picker- is a tool that identifies membrane proteins in cryo-EM micrographs by using the Segment Anything Model and integrating with cryoSPARC.

Learn more here: https://buff.ly/3Ph5Goz

#SBGrid #SBGridsoftware #Structuralbiology
GitHub - r-karimi/vesicle-picker: A program interfacing Segment Anything with cryoSPARC via cryosparc-tools to efficiently identify vesicle-embedded membrane proteins and complexes in cryo-EM micrographs.
A program interfacing Segment Anything with cryoSPARC via cryosparc-tools to efficiently identify vesicle-embedded membrane proteins and complexes in cryo-EM micrographs. - r-karimi/vesicle-picker
buff.ly
January 24, 2025 at 5:00 PM
sbgrid.bsky.social
New Title Alert: CCPEM-pipeliner- an integrated suite of software tools for processing single particle cryoEM data, from preprocessing raw image data through building and fitting atomic models.

Learn more here: buff.ly/eXK1ka2

#SBGrid #SBGridsoftware #StructuralBiology
ccpem / ccpem-pipeliner · GitLab
Python pipeliner for CCP-EM and RELION
buff.ly
July 9, 2025 at 4:05 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 Title Alert: AreTomo3- a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.

More here: https://github.com/czimaginginstitute/AreTomo3

#SBGrid #structuralbiology #SBGridsoftware
GitHub - czimaginginstitute/AreTomo3: Live processing and real time reconstruction of cryo
Live processing and real time reconstruction of cryo - czimaginginstitute/AreTomo3
github.com
September 11, 2024 at 4:00 PM
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
New Title Alert: PyTME- a software for template matching on tomographic electron microscopy data.

More here: https://github.com/KosinskiLab/pyTME

#SBGrid #SBGridsoftware #structuralbiology
GitHub - KosinskiLab/pyTME
Contribute to KosinskiLab/pyTME development by creating an account on GitHub.
github.com
September 19, 2024 at 4:00 PM
sbgrid.bsky.social
New Title Alert: AITom- an open-source platform for AI driven cellular electron cryo-tomography analysis.

Learn more here: buff.ly/LLGhjvY

#SBGrid #SBGridSoftware #StructuralBiology
Research
Xu Lab of Computational Biology
buff.ly
August 12, 2025 at 4:03 PM
sbgrid.bsky.social
New Title Alert: Glow- a versatile markdown tool offering both a text-based user interface (TUI) for interactive browsing and a command-line interface (CLI) for direct manipulation of markdown content.

Learn more here: https://buff.ly/2ZptnzW

#SBGrid #structuralbiology #SBGridsoftware
GitHub - charmbracelet/glow: Render markdown on the CLI, with pizzazz! 💅🏻
Render markdown on the CLI, with pizzazz! 💅🏻. Contribute to charmbracelet/glow development by creating an account on GitHub.
buff.ly
October 17, 2024 at 4:00 PM
sbgrid.bsky.social
New Title Alert: BindCraft- a user friendly and accurate binder design pipeline.

Learn more here: https://buff.ly/3CEqPpU

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - martinpacesa/BindCraft: User friendly and accurate binder design pipeline
User friendly and accurate binder design pipeline. Contribute to martinpacesa/BindCraft development by creating an account on GitHub.
buff.ly
February 6, 2025 at 12:00 PM
sbgrid.bsky.social
New Title Alert: TOMOMAN- a MATLAB package for managing the various preprocessing steps for taking raw data to reconstructed tomograms.

More here: https://github.com/wan-lab-vanderbilt/TOMOMAN

#SBGridSoftware #SBGrid #structuralbiology
GitHub - wan-lab-vanderbilt/TOMOMAN: A set of MATLAB wrapper scripts to help with pre-processing of tomography data.
A set of MATLAB wrapper scripts to help with pre-processing of tomography data. - wan-lab-vanderbilt/TOMOMAN
github.com
August 29, 2024 at 4:00 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
New Title Alert: Doppio- a new web-based user interface for CCP-EM and RELION software.

Learn more here: https://buff.ly/3WLnBaW

#SBGridSoftware #StructuralBiology
CCP-EM: Collaborative Computational Project for Electron cryo-Microscopy
Collaborative Computational Project for Electron cryo-Microscopy
buff.ly
February 11, 2025 at 12:00 PM
sbgrid.bsky.social
New Title AlertL: ANARCI- Antibody Numbering and Antigen Receptor ClassIfication.

Learn more here: buff.ly/i8FmJQx

#SBGrid #SBGridSoftware #StructuralBiology
GitHub - oxpig/ANARCI: Antibody Numbering and Antigen Receptor ClassIfication
Antibody Numbering and Antigen Receptor ClassIfication - oxpig/ANARCI
buff.ly
November 11, 2025 at 5:04 PM
sbgrid.bsky.social
New Title Alert: AMPLIFY- a best-in-class protein Language Model (pLM) that is orders of magnitude less expensive to train and deploy than previous models.

Learn more here: https://buff.ly/48DOu5w

#SBGrid #SBGridsoftware #structuralbiology
GitHub - chandar-lab/AMPLIFY
Contribute to chandar-lab/AMPLIFY development by creating an account on GitHub.
buff.ly
November 13, 2024 at 5:00 PM
sbgrid.bsky.social
New Title Alert: DeepETPicker- a deep learning based open-source software with a friendly user interface to pick 3D particles rapidly and accurately from cryo-electron tomograms.

More here: https://github.com/cbmi-group/DeepETPicker

#SBGridSoftware #SBGrid #structuralbiology
GitHub - cbmi-group/DeepETPicker
Contribute to cbmi-group/DeepETPicker development by creating an account on GitHub.
github.com
August 27, 2024 at 3:51 PM
sbgrid.bsky.social
New Title Alert: Follow_Relion_Gracefully- a complete dashboard for easy interaction with your cryo-EM data in Relion, now with full #teamtomo support!

Learn more here: buff.ly/SvNR5si

#SBGridsoftware #StructuralBiology
GitHub - dzyla/Follow_Relion_gracefully: New program to follow Relion projects in a browser!
New program to follow Relion projects in a browser! - dzyla/Follow_Relion_gracefully
buff.ly
June 17, 2025 at 5:06 PM
sbgrid.bsky.social
New Title Alert: BindCraft- a user friendly and accurate binder design pipeline.

Learn more here: buff.ly/GJJ6wUR

#SBGrid #SBGridSoftware #StructuralBiology
October 15, 2025 at 5:15 PM