SBGrid: Structural Biology Software

Our webinar in November, it is now available! Pavel Afonine,Ph.D. Computational Research Scientist, Berkeley Lab presented AQuaRef - Machine Learning Accelerated Quantum Refinement of Protein Structures. buff.ly/4fYPAez buff.ly/3Czqx3b #structuralbiology

New Title Alert: ChemEM- a tool that utilizes information from Cryo-EM density and state-of-the-art small molecule force fields to dock small molecules into protein targets. Learn more here: chemem.topf-group.com #SBGrid #SBGridsoftware #structuralbiology

New Member Alert: @AGhanbarpour of @WUSM_BMB has joined SBGrid in October, Welcome!

Technical Notes: MacOS Sequoia rsync to opensync issues- With the release of macOS 15 Sequoia, Apple has changed from rsync to openrsync. We have seen problems using this openrsync build with the SBGrid Installation Manager. We will soon release a new version.

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: github.com/chandar-lab/AM… #SBGrid #SBGridsoftware #structuralbiology

On November 12th, we'll hear from Pavel Afonine of @Berkeley Lab with an introduction to AQuaRef: Machine Learning Accelerated Quantum Refinement of Protein Structures. Tuesday, November 12, 2024 at 12:00pm EDT Pavel Afonine Register here: buff.ly/3AelDrK #SBGrid

Technical Notes: October's software push includes updates to cryoDRGN, CryoSieve, cyrosparc-tools, DIALS, MemBrain-Seg, PHYLIP, qFit, ShelXle, and Warp. More here: sbgrid.org/software/recen…

How cells fix broken RNA: a publication from @KeAndreya_M featuring @VincentTagliabracci, of @UTSWMedCenter Read more here: buff.ly/3YzUiYR #SBGrid #RNALigasse #structuralbiology

Pursuing a new malaria target using crystallography: a publication highlight from @VidaStormR featuring a new article from @GraemeChakafana, PhD of @_HamptonU. Read more here: buff.ly/4fx9xsI #SBGrid #Mallaria #Crystallography

New Title Alert: UDock2- an interactive multi-body protein-protein docking software that predicts the geometry of protein interactions through an intuitive real-time docking procedure with on-the-fly scoring. Learn more here: udock.fr #SBGrid #structuralbiology

@SBGrid's eLife paper received a citation in September from @WuLabHarvard of @BostonChildrens in @ScienceAdvances: Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway. Read more here: science.org/doi/full/10.11… #SBGrid

New Title Alert: RingMapper- a code for performing RING-MaP and PAIR-MaP analysis. Learn more here: buff.ly/3XS6u6Y #SBGrid #SBGridsoftware #structuralbiology

@SBGrid's eLife paper received a citation from the lab of the late William Weis of @Stanford University School of Medicine in @Science Signaling: Structural and functional effects of phosphopriming and scaffolding in the kinase GSK-3β. Read more here: science.org/doi/abs/10.112…

New Title Alert: pytom-match-pick- a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms. Learn more here: buff.ly/4f5JkBl #SBGrid #structualbiology #SBGridsoftware

@SBGrid's eLife paper received a citation in September from Lijun Sun from @BIDMChealth in European Journal of Medicinal Chemistry: Discovery of selective Orai channel blockers bearing an indazole or a pyrazole scaffold. Read more here: sciencedirect.com/science/articl… #SBGrid

New Title Alert: pyRMSD- a python package that offers RMSD calculations on large sets of structures, especially large pairwise RMSD matrices through multiple algorithmic implementations. Learn more here: buff.ly/3zvgxac #SBGrid #SBGridsoftware #structuralbiology

New Member Alert: Todd Washington from @uiowa joined @SBGrid in September. Welcome!!

New Title Alert: Protkit- a Python library for structural bioinformatics, protein engineering, & machine learning. Learn more here: buff.ly/3zI2XQE

New Member Alert: In September, Stephanie Wankowicz of @VanderbiltU joined @SBGrid. Welcome!!

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: buff.ly/2ZptnzW #SBGrid #structuralbiology