New Title Alert: DomainSeeker- a tool designed for de novo identification of protein domains in cryo-ET maps of protein complexes.
Learn more here: https://github.com/zyzhangGroup/DomainSeeker
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New Title Alert: polychrom- a tool designed to build mechanistic models - i.e. models that simulates a biological process.
Learn more here: https://github.com/open2c/polychrom
SBGrid's eLife paper received a new citation in February from Chad Rienstra and Elizabeth Wright from University of Wisconsin-Madison in bio-protocol Journal: High-resolution Cryo-EM Structure Determination of a-Synuclein—A Prototypical Amyloid Fibril.
Read more here: https://buff.ly/vHi37IO
SBGrid's eLife paper received a new citation in February from Ignacio Mir Sanchis of Umeå University in Nature Communications: Phage parasites targeting phage homologous recombinases provide antiviral immunity.
NaturePhage parasites targeting phage homologous recombinases provide antiviral immunity - Nature CommunicationsSome bacteria use anti-phage defense systems that target phage-encoded recombinases through unclear mechanisms. Here, the authors show that a transcriptional repressor encoded in a phage satellite mediates antiviral immunity by forming oligomers that bind and inhibit phage recombinases.
New Title Alert: Cryosamba- a deep learning based tool for denoising cryo-ET datasets. It is designed to accept .mrc, .rc and .tif single 3D files, or can accept a sequence of https://2D.tf files if a path is provided.
Learn more here: https://github.com/kirchhausenlab/Cryosamba
SBGrid's eLife paper received a new citation in February from member laboratories at UT Southwestern in The Journal of Clinical Investigation: An FDA-approved drug structurally and phenotypically corrects the K210del mutation in genetic cardiomyopathy models.
Read more here: https://buff.ly/F1AUbeJ
buff.lyJCI -
An FDA-approved drug structurally and phenotypically corrects the K210del mutation in genetic cardiomyopathy models
New Title Alert: GAPSTOP- is GPU-Accelerated Python STOPgap for Template Matching for fast template matching (TM) in cryo electron tomograms that is based on TM routines from STOPGAP.
Learn more here: https://gitlab.mpcdf.mpg.de/bturo/gapstop_tm
New Title Alert: CryFold- a software that automatically constructs full-atom 3D structural models of proteins based on cryo-EM density maps and sequence information.
Learn more here: https://github.com/SBQ-1999/CryFold
SBGrid's eLife paper received a citation in February from M. Gordon Joyce from The National Institutes of Health in Immunity: Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350.
Technical Notes: February's software push includes updates to AlphaFold, AmberTools, Boltz-1, DeepEMhancer, DiffDock, FPSim2, IMOD, PDBExtract, and USF Gerard Utilities.
More here: https://sbgrid.org/software/recent/archive/2025/02/
New Title Alert: LucaProt- a novel deep learning framework that incorporates protein amino acid sequence and structural information to predict protein function.
Learn more here: https://github.com/alibaba/LucaProt
A potential target for myobacteria: a publication highlight from Meharry Medical College Ph.D. candidate KeAndreya Morrison featuring a new article from the laboratory of @WeberBan_Lab of ETH Zurich.
Read more here: https://buff.ly/3c27V2w
Looking at the bacterial artillery: a publication highlight from Vida Robertson featuring a new article from Matteo Dal Peraro of École polytechnique fédérale de Lausanne, EPFL
Read more here: https://buff.ly/ScJSfbb
New Title Alert: PDBImages- a command-line tool from PDBe EMBL-EBI for generating images of macromolecular structures from mmCIF or binary CIF structure files based on Mol*.
Learn more here: https://github.com/PDBeurope/pdb-images
New Title Alert: napari-tomoslice- a plugin for napari to aid in tomogram visualisation and annotation.
Learn more here: https://github.com/alisterburt/napari-tomoslice
New Title Alert: Chai-1- a multi-modal foundation model for molecular structure prediction that performs at the state-of-the-art across a variety of benchmarks. Chai-1 enables unified prediction of proteins, small molecules, DNA, RNA, glycosylations, and more.
Learn more here: https://www.chaidiscovery.com/blog/introducing-chai-1
New Title Alert: TEMPy-ReFF- a tool that helps flexible-fitting and refinement of atomic models into cryo-EM maps.
Learn more here: https://tempy-reff.topf-group.com/
SBGrid's eLife paper received a citation in January from SBGrid members Goran Bajic from Icahn School of Medicine at Mount Sinai and Aaron Schmidt from Mass General Brigham in Science Immunology: Human naïve B cells recognize prepandemic influenza virus hemagglutinins.
New Title Alert: OpenNucleome- an open-source software designed for conducting molecular dynamics (MD) simulations of the human nucleus. This software streamlines the process of setting up whole nucleus simulations through just a few lines of Python scripting.
Learn more here: https://github.com/ZhangGroup-MITChemistry/OpenNucleome
Technical Notes: January's software push includes updates to Boltz-1, CCP4, ChimeraX,cryoDRGN, LipIDens, ProteinMPNN, PyMOL, Python, R, Topaz, Schrodinger, and Warp.
More here: https://sbgrid.org/software/recent/archive/2025/01/
sbgrid.orgSBGrid Consortium - Software UpdatesThe 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 computing.