easymode

New Title Alert: easymode- a collection of general pretrained networks for cellular cryoET.

Learn more here: buff.ly/mLbcUbZ

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GitHub - Kuhlman-Lab/ThermoMPNN: GNN trained to predict changes in thermodynamic stability for protein point mutants GNN trained to predict changes in thermodynamic stability for protein point mutants - Kuhlman-Lab/ThermoMPNN

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

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GitHub - CellArchLab/slabify-et: A CLI tool to segment the lamella slab in cryo-ET volumes A CLI tool to segment the lamella slab in cryo-ET volumes - CellArchLab/slabify-et

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

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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

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GitHub - polizzilab/LASErMPNN: All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN - polizzilab/LASErMPNN

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

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GitHub - oxpig/ImmuneBuilder: Predict the structure of immune receptor proteins Predict the structure of immune receptor proteins. Contribute to oxpig/ImmuneBuilder development by creating an account on GitHub.

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

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SBGrid Consortium - Software Updates The 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…

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

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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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GitHub - Rostlab/ConSurf: Evolutionary conservation estimation of residues or nucleotides Evolutionary conservation estimation of residues or nucleotides - Rostlab/ConSurf

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

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GitHub - mariacarreira/calc_level_ChimeraX: ChimeraX command to predict isosurface levels for 3D density maps ChimeraX command to predict isosurface levels for 3D density maps - mariacarreira/calc_level_ChimeraX

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

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GitHub - Kuhlman-Lab/ThermoMPNN-D: Extension of ThermoMPNN for double mutant predictions Extension of ThermoMPNN for double mutant predictions - Kuhlman-Lab/ThermoMPNN-D

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

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GitHub - ccameron/REPIC: REliable PIcking by Consensus (REPIC) - an ensemble learning methodology for cryo-EM particle picking REliable PIcking by Consensus (REPIC) - an ensemble learning methodology for cryo-EM particle picking - ccameron/REPIC

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

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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

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GitHub - rs-station/meteor: bringing you the best difference maps bringing you the best difference maps. Contribute to rs-station/meteor development by creating an account on GitHub.

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

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SBGrid Consortium - Software Updates The 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…

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

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GitHub - yehlincho/Protein-Hunter Contribute to yehlincho/Protein-Hunter development by creating an account on GitHub.

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

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CryoSiam Documentation Welcome to the official documentation for the CryoSiam method. This guide will help to use this tool effectively.

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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cryoCAT: Contextual Analysis Tools for cryo electron tomography — cryoCAT 0.2.2 documentation Site Navigation

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

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GitHub - YangLab-SDU/CryoAtom: From cryo-EM density map to atomic structure From cryo-EM density map to atomic structure. Contribute to YangLab-SDU/CryoAtom development by creating an account on GitHub.

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

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SBGrid Consortium - Software Updates The 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…

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

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GitHub - bionanopatterning/Pom: Scaling data analyses in cellular cryoET using comprehensive segmentation. Scaling data analyses in cellular cryoET using comprehensive segmentation. - bionanopatterning/Pom

New Title Alert: Pom- a tool for scaling data analyses in cellular cryoET using comprehensive segmentation.

Learn more here: buff.ly/qisPeYQ

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Molecular Modeling Software | OpenEye Scientific Molecular modeling and cheminformatics software tools built in the cloud to accelerate lead discovery and optimization in drug development.

New Title Alert: OpenEye Academic Package- tools to help design potent and selective bioactive molecules.

Learn more here: buff.ly/SMacQQa

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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

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GitHub - swing-research/icecream: 🍦Icecream: a self-supervised framework for cryo-ET reconstruction 🍦Icecream: a self-supervised framework for cryo-ET reconstruction - swing-research/icecream

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

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GitHub - apple/ml-simplefold Contribute to apple/ml-simplefold development by creating an account on GitHub.

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

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SBGrid Consortium - Software Updates The 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…

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

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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

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GitHub - yehlincho/BoltzDesign1 Contribute to yehlincho/BoltzDesign1 development by creating an account on GitHub.

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

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GitHub - oxpig/ANARCI: Antibody Numbering and Antigen Receptor ClassIfication Antibody Numbering and Antigen Receptor ClassIfication - oxpig/ANARCI

New Title AlertL: ANARCI- Antibody Numbering and Antigen Receptor ClassIfication.

Learn more here: buff.ly/i8FmJQx

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GitHub - alisiafadini/ROCKET Contribute to alisiafadini/ROCKET development by creating an account on GitHub.

New Title Alert: ROCKET- is a tool for refining AlphaFold predictions using crystallographic and cryo-EM likelihood targets.

Learn more here: buff.ly/s9y4bFV

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