MD Simulations for Williams B.G., et. al. (2025)

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