Viktoria Korn

Abstract

The simulation files, molecule topologies, and analysis workflows required to generate the results of our paper 'ART-SM: Boosting Fragment-Based Backmapping by Machine Learning' published in J. Chem. Theory Comput..In details:simulations.tar.gz: Contains the pdb (molecular structure), xtc (trajectory), mdp (MD parameters), itp (topology), and top (topology) files. GROMACS 2021 or 2023 was used for the simulations (see paper for details). Additionally, ART-SM mapping files (generated with version 1.0) and Backward mapping files from coarse-grained to atomistic resolution are included.workflows.tar.gz: Snakemake was used to handle the analysis workflows. The corresponding Snakefiles and python/bash scripts to reproduce the results in the paper are included. The actual results are not included (see paper instead). The main packages required for reproducing the results are listed under 'Software Metadata - Software Requirements'. If a second version is specified it was used only for 'sds_capb_section_4_4'. The first specified version was used for all other analyses.Please have a look at the README files contained in each .tar.gz file.

Abstract

Simulation files, molecular structures and trajectories, and jupyter notebooks used for analysis underlaying our publication on membrane insertion of monomeric gasdermin D to E. coli polar lipid extract (PLE). In detail: charmm36-july2017.ff simulation directory for GROMACS 202X, used and useful gromacs files (topologies and mdp files),jupyter notebooks for analysis, snapshots and trajectories of monomeric gasdermin D in E. coli PLE, including umbrella sampling simulations, snapshots and trajectories of monomeric gasdermin D in POPC/30%cholesterol, snapshots and trajectories of arcs of seven gasdermin D subunits in E. coli PLE.