2025/11/20 by Cagiada, Matteo, Spoendlin, Fabian Christopher, Deane, Charlotte +1 · 1 voice
paper · doi:10.5281/zenodo.17648294
openalex publication_date 2025/11/20 · openalex created_date 2025/11/28 · openalex updated_date 2026/07/01
This repository contains molecular dynamics (MD) simulation data associated with the publication "Uncovering the flexibility of CDR loops in antibodies and TCRs through large-scale molecular dynamics" (Cagiada M, Spoendlin F.C - 2025). The data provided here include MD trajectories and topologies files generated using CALVADOS 3 Fv (CV3Fv) for all experimentally resolve structure of antibodies and T-cell receptors (TCRs) present in FlAbDab and FTCRDab. For each system we include: coarse grain trajectory (.dcd), all-atom trajectory (.xtc, converted with cg2all), topologies, input files and a set of representative structure for each system. Please refer to the manuscript for additional methodological details. Simulations were performed using CALVADOS 3 with a custom set of restraint, in a setup named CV3Fv. Simulation productions were run at 298 K for 100ns in total. Please refer to the manuscript for additional methodological details. N.B: All-atom trajectories may include clashes resulting from the conversion process. If you wish to analyse the trajectory, we recommend using the coarse-grain file.