Frequently Asked Questions

Yes. Currently, we only support output from the AlphaFold Server. We are actively working to add support for other structure prediction algorithms, including locally installed versions of AlphaFold3, AlphaFold-Multimer, and ColabFold. Follow us on social media for updates on these new features. If you need support for other structure prediction algorithms, please contact us, and we will do our best to assist you.

AlphaBridge currently supports predictions containing Protein, DNA, and RNA. Ligands and modified residues or nucleotides are not yet supported and will disrupt the analysis if included. Support for those compounds will be added in the (near) future. Stay connected on social media for the latest news.

AlphaBridge analyzes only the top-ranked model predicted by AlphaFold.

Do not unzip and recompress the file as this may cause submission errors.

Yes, the “backend” code that does the calculations and produces data and static plots, along with setup instructions and environment configuration, is available in our public repository at https://github.com/PDB-REDO/AlphaBridge. This includes detailed guidance on installation and usage.

No, the “frontend” code for the AlphaBridge website itself is not publicly available. If you want a local (private) installation get in contact though.

For any enquiries and feedback, please refer to the contact section on our website.

Please reference our paper: Álvarez-Salmoral, D. et al. (2024) Alphabridge: Tools for the analysis of predicted macromolecular complexes [Preprint]. doi:10.1101/2024.10.23.619601.