ctboughter/aims_manuscripts

This is a repository for the explicit replication of AIMS analysis published in a range of manuscripts

AIMS - An Automated Immune Molecule Separator

Description

This particular repository is specifically for recreating the analysis in all manuscripts published thus far using AIMS. If you'd like to use AIMS to run your own analysis, please see:

https://github.com/ctboughter/AIMS

The AIMS github has its own programmed tutorials, whereas the jupyter notebooks provided in this repository give step-by-step recreation of figures in each individual manuscript.

Further Reading

Now that AIMS has been out and in the wild for around two years, there have been additional published peer-reviewed manuscripts or posted preprints that highlight the capabilities of AIMS! I'll try to keep this list relatively up to date, and if it ever gets lengthy will likely move it to the ReadTheDocs page. Manuscripts thus far include:

• The original AIMS paper, with an application of AIMS to the problem of antibody polyreactivity: https://elifesciences.org/articles/61393
• An application of AIMS to non-immune molecules using multi-sequence alignment (MSA) encoding: https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.2c02173
• The AIMS bible, with a thorough explanation of the rationale behind the AIMS analysis: https://www.biorxiv.org/content/10.1101/2022.12.07.519510v1
• An investigation of the nature of the germline interactions between TCR CDR loops and MHC: https://www.biorxiv.org/content/10.1101/2022.12.07.519507v1

Documentation

Rather than have all of the instructions on this GitHub page, all information on installation and usage (and more!) has been moved to a separate, more readable documentation page. Please follow this link:

https://aims-doc.readthedocs.io/en/latest/

For the comprehensive AIMS user guide.