Author: Matteo Cagiada
Date: October 2025
Version: v1.0
Contact: matteo.cagiada@io.ku.dk / matteo.cagiada@stats.ku.dk
This repository accompanies the paper:
Structural basis for synergistic antibody protection against the essential malaria invasion complex protein RIPR
Barnabas G. Williams; Jordan R. Barrett; Josefin Bartholdson Scott; Cassandra A. Rigby; Matteo Cagiada; Doris Quinkert; Kirsty McHuhh; Anna Huhn; Sean A. Burnap; Camille Gourjault; Francesca Byrne; Sai Sundar Rajan Raghavan; Ana Rodrigues; Laura Bergamaschi; Beatrice Balzarotti; Simon Watson; Noah Miller; Lloyd D.W. King; Francesca R. Donnellan; Camilla Gladstone; Jemima Paterson; Stefania Scalabrino; Sarah E. Silk; Jo Salkeld; Angela M. Minassian; Katherine Skinner; Weston B. Strewe; Charlotte M. Deane; Stephen T. Reece; Andrew B. Ward; Simon J. Draper
This repository includes jupyter notebook used to run the analyse and make figures for the molecular dynamics (MD) simulations of RIPR referenced in the main manuscript.
All results can be reproduced following the instructions below.
Download all MD trajectories from the Zenodo repository:
🔗 DOI: 10.5281/zenodo.17315520
Place all downloaded files in the src folder located in the main directory of this repository.
- Python version: 3.9+
- Recommended environment: Conda
The following Python packages are required:
numpy MDAnalysis seaborn matplotlib scipy itertools scikit-learn
Open the notebook in Jupyter and execute all cells in order:
jupyter notebook TSNE_analysis.ipynbThe sections, variables, and figures in the notebook are labeled according to chain identifiers in the crystal structure.
Below is a mapping between the simulation names used in the notebook and the corresponding system compositions:
| Notebook Label | System Description |
|---|---|
| ripr_all_domain | RIPR + RP.035 + RP.047 + RP.057 + RP.063 + RP.073 + RP.093 |
| ripr_LM_HI_JK_domain | RIPR + RP.035 + RP.047 + RP.057 |
| ripr_HI_JK_DE_domain | RIPR + RP.052 + RP.047 + RP.057 |
| ripr_BO_CD_EF_domain | RIPR + RP.063 + RP.073 + RP.093 |
| ripr_LM_JK_domain | RIPR + RP.035 + RP.057 |
| ripr_HI_JK_domain | RIPR + RP.047 + RP.057 |
| ripr_LM_BO_domain | RIPR + RP.035 + RP.093 |
| ripr_LM_domain | RIPR + RP.035 |
| ripr_HI_domain | RIPR + RP.047 |
| ripr_JK_domain | RIPR + RP.057 |
| ripr_BO_domain | RIPR + RP.093 |
| ripr_DE_domain | RIPR + RP.052 |
| ripr_only | RIPR alone |
For questions, feedback, or issues reproducing results in this notebook:
📧 matteo.cagiada@io.ku.dk / matteo.cagiada@stats.ku.dk
For questions or feedback on the manuscript:
📧 simon.draper@bioch.ox.ac.uk /
If you use this notebook or associated data, please cite:
Williams et al., Structural basis for synergistic antibody protection against the essential malaria invasion complex protein RIPR, VeriXiv, 2025
## ⚖️ License
This repository and associated notebooks are distributed under the **MIT License**.