Software
CueMol
CueMol is software for viewing the structure of biological macromolecules. We are developing a user interface that is seamless and easy to understand with the GUI of the operating system. In addition, CueMol is capable of producing high-quality molecular graphics for publications and presentations.
LocalColabFold
https://github.com/YoshitakaMo/localcolabfold/
LocalColabFold is an installer script designed to make ColabFold functionality available on users’ local machines. It supports wide range of operating systems, such as Windows 10 or later (using Windows Subsystem for Linux 2), macOS, and Linux.
alphafold3_tools
https://github.com/cddlab/alphafold3_tools/
alphafold3_tools is a collection of tools for AlphaFold3. It includes various scripts such as msatojson, a convertor of MSA file to the input JSON file for AlphaFold3, and paeplot, a script to visualize a predicted aligned error (PAE), and so on.
RGI-toolkit
https://github.com/cddlab/rgi_toolkit
RGI-toolkit (Restraint-Guided Inference toolkit) introduces differentiable restraints into diffusion-based biomolecular structure predictors. By applying distance, angle, RMSD, conformer, and other restraints during the denoising process, it enables controllable structure prediction. It supports models such as Boltz-1/2, AlphaFold3, Protenix, ESMFold2, OpenFold-3, Chai-1, and RF3, and can also be used from ColabFold notebooks.