MD Simulations for Williams B.G., et. al. (2025)
Authors/Creators
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1.
University of Copenhagen
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2.
University of Oxford
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3.
Scripps Research Institute
Description
Supplementary Information for MD simulations in: Williams B.G., et.al. (2025)
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 jall the molecular dynamics (MD) simulations of RIPR referenced in the main manuscript.
To reproduce the results and figures in the manuscriptusing the simulation in this repository please follow the instruction in the GitHub repository: https://github.com/matteo-cagiada/_2025_Williams_RIPR.
🧩 Simulation System Naming
The molecular dynamics simulations stored in this repository 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:
| MD 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 |
Files
ripr_all_domain.zip
Files
(29.2 GB)
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Additional details
Funding
- Bill & Melinda Gates Foundation
- Isolation of anti-RH5/CyRPA/RIPR/RCR-complex mAbs INV-030873
- Novo Nordisk Foundation
- A study on proteins’ dynamics and conformational changes using large language models NNF23OC0082912
Software
- Repository URL
- https://github.com/matteo-cagiada/_2025_Williams_RIPR
- Development Status
- Active