AlphaPulldown 2.4.0 includes fixes across the multimer workflow with mmseqs2 TrueMultimer custom template support, reuse of existing monomer features in the default TrueMultimer mode, and skip-MSA feature generation in the AF2/mmseqs2/AF3 data pipeline. It also corrects AF3 trimer pairing logic when running the AF3 backend with AF2-derived features and resolves multiple reported issues affecting robustness and feature generation.
https://github.com/KosinskiLab/AlphaPulldown/releases/tag/2.4.0
Avogadro 2.0.0 features a complete rewrite that improves speed and stability, allowing the software to handle systems with hundreds of thousands of atoms using a modern 3D rendering engine. Key additions include a flexible layer system for organizing molecular components, a Template tool for rapidly building complex geometries, and advanced visualization options like real-time shadows, volumetric orbitals, and non-bonded interaction analysis. The update also introduces a powerful Python-based plugin architecture and Jupyter integration, making it much easier to extend the software's capabilities and interface with external computational chemistry programs.
https://github.com/OpenChemistry/openchemistry/releases/tag/2.0.0
BioEmu 1.3.0 includes improved structure-generation and refinement workflows, notably steering to reduce chain breaks and clashes and inlining ColabFold and AlphaFold2 into BioEmu. The release also updates OpenMM, removes the disulfide potential, writes the physics-filtered frame to topology.pdb, and makes testing faster and more informative through accelerated md-relaxation tests and pytest duration reporting.
https://github.com/microsoft/bioemu/releases/tag/v.1.3.0
BioEmu 1.3.1 is a minor bug fix update.
https://github.com/microsoft/bioemu/releases/tag/v1.3.1
ChemEx 2026.04.0 includes composable residue-specific kinetic-model suffixes such as .rs with .mf and .tc, broader residue-specific parameter naming, and a refactored chemex.nmr architecture that separates engine, pulse, B1, detection, effective-field, magnetization, and tensor components. It also fixes output-file naming collisions across datasets, strengthens parsing and validation for constraints, grids, TOML configs, B1 inhomogeneity, and shift/R1rho calculations, and expands regression coverage for NMR engine behavior and residue-specific models.
https://github.com/gbouvignies/ChemEx/releases/tag/v2026.04.0
ColabFold 1.6.0 includes AlphaFold3-compatible JSON export, a redesigned MSA pairing pipeline for complex predictions, warm-starting from initial structures, GPU-accelerated MMseqs2 search, and expanded control over templates, logging, and output generation. The release also improves deployment and performance with lighter colabfold_search dependencies, faster MSA deserialization, updated Docker support, AWS S3 database downloads, a switch to PDB100 template search, and ARM64 pip installability. Additional changes add actifpTM scoring, optional faster JSON serialization, and per-entry custom templates in CSV input, alongside fixes for CSV parsing, database download retries, query unpacking, multimer template databases, and protein-sequence handling.
https://github.com/sokrypton/ColabFold/releases/tag/v1.6.0
ColabFold 1.6.1 fixes some minor bugs.
https://github.com/sokrypton/ColabFold/releases/tag/v1.6.1
CryoAtom 2.1.0 includes multi-GPU inference support, enabling inference workflows to scale across multiple GPUs. This release also fixes hmm_search cases that could yield empty identifications, improves robustness to certain FASTA input formats, and increases RU-Net iterations from 1 to 3.
https://github.com/YangLab-SDU/CryoAtom/releases/tag/v2.1.0
fold_tree 1.1.0 includes a refactor of v1.0.0 that adds the foldtree script as a black-box entry point for running the Snakemake pipeline and restructures the project for installation. This release also adds a Python wrapper for the main workflow, splits and minimizes conda dependencies, and introduces a configurable `--conda-prefix` with Snakemake environments defaulting to `~/.foldtree` to avoid redundant environment recreation across working directories.
https://github.com/DessimozLab/fold_tree/releases/tag/v1.1.0
OpenFold3 0.4.1 includes native AMD ROCm inference via Triton kernels, extending inference support to AMD hardware. It also fixes arginine naming, chain-template alignment labeling, symmetric-chain permutation alignment with unresolved residues, checkpoint configuration, multi-user /tmp permission errors, and invalid JSON output, while adding cif.gz structure support and improved environment and contribution documentation.
https://github.com/aqlaboratory/openfold-3/releases
PyMOL 3.1.8 is the latest version of the popular molecular visualization system, offering improved rendering, animations, and full Python 3.10 integration. This release features a refined interface with enhanced mouse controls, making rotation, zooming, and clipping more intuitive and advanced visualization tools for protein surfaces, molecular dynamics trajectories, and high-quality, publication-ready graphics across all major platforms.
https://www.pymol.org/
Relion 5.1.0-beta implements new functionality for amyloid filaments. A new auto-picker that specifically detects the 4.75A signal in the Fourier transform of micrographs, amyprep and amyproc Schemes for the automated pre-processing of amyloid data sets, and a retrained version of the Blush regularisation denoising network that is specific for amyloid filaments. This release also implements minor updates to the tomography pipeline, including a wrapper to AreTomo2's tomogram reconstruction algorithm, an option to extract real 3D subtomograms (this goes well with the AreTomo2 reconstructions) and use these for 3D classifications/refinements.
https://github.com/3dem/relion/releases
Scipion 3.11.6 updates the scipion-em (core) to 3.11.0, which includes new protocols to crop and resize volumes, filter by normal, and break symmetry. New image readers include gain and dark files from Gatan camera (.dm3, .dm4) and .em files (based on the standard TOM toolbox header structure, e.g. Dynamo). This version updates the CryosSPARC plugin configuration in Scipion and the latest release versions for Tomo (core), Topaz, Imod, Dynamo, Gapstop, Aretomo and MotionCorr plugins, which mainly consists on bugfixing.
TomoNet 1.06 is the new default version. No release notes are available.
https://github.com/logicvay2010/TomoNet/releases/tag/V1.06
