Computational data on binding of a pyrene-based fluorescent amyloid ligand (Py1SA) to transthyretin (TTR)

This repository contains the data and files for the computational study on binding of a pyrene-based fluorescent amyloid ligand (Py1SA) to transthyretin (TTR). <br> The repository is organized into different folders as described below: ====================================================================================================<br> 1_Starting_structure<br> This folder contains the starting structures of the four binding modes obtained from the crystallographic study. These structures serve as the initial configurations for the Molecular Dynamics (MD) simulations. ====================================================================================================<br> 2_mdp_files<br> This folder contains two subfolders: 1_MD<br> The "1_MD" subfolder includes the MD simulation files in the mdp format. These files define the parameters and settings for running the MD simulations with Gromacs version 2019.3. 2_US<br> The "2_US" subfolder includes the files required for performing Umbrella Sampling (US) simulations for each of the binding modes using Gromacs version 2021.3. Within each mode folder, you will find the following files: constraint: Position restraints files used in the Umbrella Sampling simulations.<br> pull: mdp files containing the settings for pulling in the US simulations.<br> us: mdp files used for the US simulations. ====================================================================================================<br> 3_MD_results<br> This folder contains the results of the MD simulations. It includes the structure files (.gro) and trajectory files (.xtc) for each simulation. Due to the large size of the files, the solvent has been excluded, and the results are provided at every 1 nanosecond (ns) interval. ====================================================================================================<br> 4_US_results<br> The "4_US_results" folder includes the trajectories of the US simulations for each of the binding modes. For each mode, two trajectories are provided. ====================================================================================================<br> 5_pdb<br> This folder includes the pdb files of the simulated structures of the two binding modes after the equilibration step. ==================================================================================================== We acknowledge funding by the German Research Foundation (DFG) through the Emmy Noether Young Group Leader Programme (CK, project KO 5423/1-1), the Swedish e-Science Research Centre (SeRC, ML, PN), the Swedish Research Council (PN, Grant No. 2018-4343). Computing resources were provided by the Swedish National Infrastructure for Computing (SNIC).