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
#SBGrid #SBGridSoftware
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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New Title Alert: easymode- a collection of general pretrained networks for cellular cryoET.
Learn more here: buff.ly/mLbcUbZ
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New Title Alert: ThermoMPNN- is a graph neural network (GNN) designed to predict changes in stability for protein point mutants using transfer learning.
Learn more here: buff.ly/cXIXkW8
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: Slabify- is a command-line tool designed for the automatic segmentation of lamella slabs in cryo-electron tomography (cryo-ET) volumes.
Learn more here: buff.ly/fVsKsOS
#SBGrid #SBGridSoftware
New Title Alert: MagCalEM- Accurate magnification determination for cryoEM determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximise resolution and enable accurate model building.
Learn more here: buff.ly/vuCrtWR
#SBGridSoftware #SBGrid
New Title Alert: LASErMPNN- is an all-atom ligand-conditioned protein sequence design and sidechain packing model that accounts for the presence of small molecules, including hydrogens.
Learn more here: buff.ly/cZcOmpC
#SBGridSoftware #SBGrid #StructuralBiology
New Title Alert: ImmuneBuilder- is a high-performance deep learning framework developed by the Oxford Protein Informatics Group (OPIG) specifically for predicting the 3D structures of immune receptor proteins.
Learn more here: buff.ly/wCaRFLp
#SBGrid #SBGridSoftware #StructuralBiology
Technical Notes: January's software push includes updates to 15 titles -- anvi’o, BioXTAS RAW, ChemEx, CryomaskR, DeepRank-GNN-esm, DSSR, GROMACS, Icecream, IMP, PowerFit, PyEM, RDKit, SRAToolkit, Volume_Seg_Tool, and XDS.
More here: buff.ly/4ZaSgEV
#SBGridSoftware #Updates
New Title Alert: Foundry- is a unified framework for protein design that provides tooling and infrastructure for using and training models.
Learn more here: buff.ly/2TdjDOE
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New Title Alert: ConSurf- is a bioinformatics tool designed for estimating the evolutionary conservation of amino and nucleic acid positions in protein, DNA, and RNA molecules.
Learn more here: buff.ly/ormnLqE
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: Calc_level_chimeraX- is a ChimeraX plugin to predict and visualize isosurface levels for 3D density maps.
Learn more here: buff.ly/8tWjgTF
#SBGridSoftware #SBGrid #StructuralBiology
New Title Alert: ThermoMPNN-D- is a Siamese neural network designed to predict stability changes from protein double point mutations.
Learn more here: buff.ly/rogxB7G
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: REPIC- REliable PIcking by Consensus (REPIC) is a consensus methodology for harnessing multiple cryogenic-electron microscopy (cryo-EM) particle picking algorithms.
Learn more here: buff.ly/cCqyNHx
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: cryomaskR- is a desktop application that provides WYSIWYG mask generation for cryo-electron microscopy data analysis.
Learn more here: buff.ly/MC0uNqR
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: meteor- a tool for computing crystallographic difference maps that specializes in robust identification of weak signals from minor populations such as bound ligands or time-resolved experimental changes.
Learn more here: buff.ly/bgJYF9N
#SBGrid #SBGridSoftware #StructuralBiology
Technical Notes: This month's software push includes updates to BioEmu, BoltzGen, ChimeraX, DOCK, Google Cloud SDK, HADDOCK3, NAMD, OpenFold, ORCA, pytom-match-pick, pyTME, SamTOOLS, Schrödinger 2025-3 and 2025-4, and Topaz.
More information here: buff.ly/lgtNHCd
#SBGrid #SBGridSoftware
New Title Alert: Protein-Hunter- a tool for exploiting structure hallucination within diffusion for protein design. A fast, fine-tuning-free framework for de novo protein design.
Learn more here: buff.ly/DrCDsKH
#SBGrid #StructuralBiology #SBGridSoftware
New Title Alert: CryoSiam- a self-supervised deep learning framework that works on dense and subtomogram levels.
Learn more here: buff.ly/xt1uGJt
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New Title Alert: CryoCAT- an open source, GPL-3.0+ licensed library providing contextual analysis tools for cryo electron tomography and subtomogram averaging.
Learn more here: buff.ly/ug59jUR
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: CryoAtom- is a software that automatically constructs full-atom 3D structural models of proteins based on cryo-EM density maps and sequence information.
Learn more here: buff.ly/gjVyH1m
#SBGrid #SBGridSoftware #StructuralBiology
Technical Notes: This month's software push includes updates to BCFTools, BioXTAS RAW 2, CCPEM-Pipeliner, CNIO relion_tools, COOT, Doppio, OpenEye, RDKit, Scipion, and Surface-morphometrics.
More here: buff.ly/SS4Qn0w
#SBGrid #SBGridSoftware
New Title Alert: Pom- a tool for scaling data analyses in cellular cryoET using comprehensive segmentation.
Learn more here: buff.ly/qisPeYQ
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: OpenEye Academic Package- tools to help design potent and selective bioactive molecules.
Learn more here: buff.ly/SMacQQa
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: nvMolKit- is a CUDA-backed Python library for accelerating common RDKit molecular operations through batch-oriented GPU processing.
Learn more here: buff.ly/pqV1HiF
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: Icecream- a self-supervised framework for cryo-ET reconstruction that integrates equivariance principles from modern imaging theory into a deep-learning architecture.
Learn more here: buff.ly/bdepEUm
#SBGrid #SBGridSoftware #StructuralBiology
New Title Alert: SimpleFold- is the first flow-matching based protein folding model that uses only general purpose transformer layers, without relying on expensive modules like triangle attention or pair representation biases.
Learn more here: buff.ly/bfv8nwT
#SBGrid #SBGridSoftware
Technical Notes: October's software push includes updates to ChimeraX, DeepRank-GNN-ESM, MDAnalysis, NGLView, NmrPipe, Open Force Field Toolkit, Open Free Energy, PowerFit, PyTOM-match-pick, RDKit, and TomoNet.
More here: buff.ly/uLpQznY
#SBGridSoftware #SBGridUpdates
New Title Alert: CTFMeasure- a software for estimating CTF parameters of cryo-ET tilt series. It features tilt-series-based joint estimation and Thon ring rescaling technique.
Learn more here: buff.ly/zh57gUB
#SBGrid #SBGridSoftware #StructuralBiology
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
