IgG1 Analysis Tools: AlphaFold Y-Shape Studio for screening AlphaFold 3 antibody models

Abstract

AlphaFold Y-Shape Studio 1.4.0 is a desktop application for screening AlphaFold 3 IgG1 antibody models and inspecting their structures with Matplotlib. It assigns chains and domains, measures hinge and Fab/Fc geometry, reports candidate disulfide bonds, and provides an interactive three-dimensional preview. Analysis runs locally. Changes in version 1.4.0 Accepts arbitrary, case-insensitive CIF filenames. Optional seed- and sample- metadata may be read from filenames or enclosing folders. Models are processed in numeric seed/sample order, and files without numbered metadata follow the numbered models. Reads the first coordinate model directly from mmCIF without an intermediate PDB file. Multi-character author chain IDs, insertion codes, and mmCIF coordinate precision are retained by the analysis reader. Reopens completed and partial runs in read-only mode. Version 1.4 previews are embedded in run_summary.json and remain available if the original CIF files are moved; version 1.3 tables also reopen, with previews rebuilt when their original CIF files remain accessible. The screening criteria and thresholds are unchanged from version 1.3.0. Downloads Windows: AlphaFold_Y_Shape_Studio_Windows_x86_64_v1.4.0.zip contains the ready-to-run executable and bundled runtime. Extract the entire ZIP, keep the _internal folder beside the executable, and double-click AlphaFold_Y_Shape_Studio.exe. Python is not required. The executable is unsigned; do not disable operating-system security protections. Linux and source: AlphaFold_Y_Shape_Studio_Source_v1.4.0.tar.gz contains the source, pinned requirements, setup and launch scripts, regression tests, build scripts, licenses, and sample. Python 3.10 with Tk, venv support, and a desktop display is recommended. Run ./scripts/setup_ui_env.sh once and then ./run_ui_from_source.sh. Later launches need only the second command. The first setup requires internet access. Both archives include the complete 15-model sample dataset with its AF3 JSON files, dependency notices, and the same README.md. The general README.md is also supplied separately. Validation and limitations Version 1.4.0 passed 86 regression tests on each tested platform: Windows 11 x64 with Python 3.10.4 and Ubuntu 22.04.2 under WSL2/WSLg with Python 3.10.12, using NumPy 2.2.6, Biopython 1.88, and Matplotlib 3.10.9. The bundled Windows executable was tested with Python absent from PATH. Default and AF3 JSON sample runs each analyzed all 15 structures with 3 passing and 0 failed inputs. Testing also covered numeric seed/sample ordering, arbitrary Unicode filenames, direct mmCIF reading, saved-run reopening, invalid inputs, cancellation, output preservation, UI interaction, and image export. This software is a geometric screening heuristic, not experimental validation of structure, function, or biological activity. Additional profiles are retained, but execution on the antibody sample does not establish their scientific classification accuracy. Other operating systems, Linux distributions, Python versions, and hardware configurations have not been exhaustively tested. No standalone Linux binary or tested container image is supplied.