Predicting the effect of amino acid mutations on protein stability using MELD-accelerated molecular dynamics simulations

This Zenodo record contains the complete dataset and software accompanying the manuscript: Predicting the Effect of Amino Acid Mutations on Protein Stability Using MELD-Accelerated Molecular Dynamics Simulations The repository enables full reproduction of the molecular dynamics simulations and analysis used to predict protein stability changes (ΔΔG) upon single amino acid mutations using MELD (Modeling Employing Limited Data). The dataset includes: Input structures for 7 proteins and 35 single amino acid mutationsWild-type and mutant protein structuresUnfolded starting structures for MELD simulationsAlphaFold-derived distance restraints and radius of gyration restraintsComplete raw MELD simulation outputs for every mutationA summary table comparing predicted and experimental ΔΔG values The repository also contains: Scripts for setting up MELD simulationsAnalysis scripts for computing ΔΔG from simulation trajectoriesThe MELD software distribution used in this study The directory structure is organized into separate data and code directories to facilitate reproducibility. A detailed README documents the repository organization, file formats, workflow, and instructions for reproducing the simulations and analysis. If you use this dataset or software, please cite the accompanying manuscript and the MELD software publication described in the repository documentation.