| _version_ | 1866902098239553536 |
|---|---|
| author | Choutka, Jan |
| author_facet | Choutka, Jan |
| contents | <p>Simulation data for a manuscript: "Molecular Symmetry Directs Ligand Orientation and Thermodynamics in Galectin-3". This dataset contains data from the molecular dynamics (MD) and replica exchange with solute tempering (REST) simulations of a symmetry-resolved series of ligands binding to Galectin-3, and the analyses of the protein-ligand interaction energies and conformational perturbations of the protein.</p> <p>The content of the folders is as follows:</p> <p><strong>code</strong>: Python code used to run the MD and REST simulations in OpenMM and analyze the trajectories.</p> <p><strong>structures</strong>: Initial structures of the protein and ligands used for the simulations. These models are based on the PDB 5H9P crystal structure.</p> <p><strong>trajectories</strong>: Contains subfolders with the trajectories for each simulated system. Each subfolder contains trajectory files in DCD format with simulation ensembles pruned to 10, 50, 100, and 1000 frames, and both the unsolvated and solvated systems in PDB and PRMTOP formats. Additional subsubfolders contain the calculated per-residue and per-atom decompositions of force field interaction energies, conformational perturbations between holo and apo states, and extracted simulation ensembles of the ligands from the holo trajectories.</p> <p><strong>CSP</strong>: The data of chemical shift perturbation (CSP) of the galectin-3 backbone nitrogens, provided as a CSV file and PDB trajectories with the CSP mapped in the B factor column.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17559339 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Simulation data: Molecular Symmetry Directs Ligand Orientation and Thermodynamics in Galectin-3 Choutka, Jan <p>Simulation data for a manuscript: "Molecular Symmetry Directs Ligand Orientation and Thermodynamics in Galectin-3". This dataset contains data from the molecular dynamics (MD) and replica exchange with solute tempering (REST) simulations of a symmetry-resolved series of ligands binding to Galectin-3, and the analyses of the protein-ligand interaction energies and conformational perturbations of the protein.</p> <p>The content of the folders is as follows:</p> <p><strong>code</strong>: Python code used to run the MD and REST simulations in OpenMM and analyze the trajectories.</p> <p><strong>structures</strong>: Initial structures of the protein and ligands used for the simulations. These models are based on the PDB 5H9P crystal structure.</p> <p><strong>trajectories</strong>: Contains subfolders with the trajectories for each simulated system. Each subfolder contains trajectory files in DCD format with simulation ensembles pruned to 10, 50, 100, and 1000 frames, and both the unsolvated and solvated systems in PDB and PRMTOP formats. Additional subsubfolders contain the calculated per-residue and per-atom decompositions of force field interaction energies, conformational perturbations between holo and apo states, and extracted simulation ensembles of the ligands from the holo trajectories.</p> <p><strong>CSP</strong>: The data of chemical shift perturbation (CSP) of the galectin-3 backbone nitrogens, provided as a CSV file and PDB trajectories with the CSP mapped in the B factor column.</p> |
| title | Simulation data: Molecular Symmetry Directs Ligand Orientation and Thermodynamics in Galectin-3 |
| url | https://doi.org/10.5281/zenodo.17559339 |