What does this research mean for the field?

Molecular dynamics simulations and MM/GBSA calculations characterize the binding dynamics, thermodynamics, and hydrogen bond interactions of Compound 41 with BACE1. Novelty: ClaimNovelty.METHODOLOGICAL. Consensus alignment: ConsensusAlignment.NEUTRAL.

What question did this study set out to answer?

The aim is to present a complete dataset from Molecular Dynamics simulations and MM/GBSA calculations for Compound 41.

May 16, 2026Open Access

Dataset of Molecular Dynamics Simulation and MM/GBSA Calculation of Compound 41

Key Points

The aim is to present a complete dataset from Molecular Dynamics simulations and MM/GBSA calculations for Compound 41.
Included raw and processed trajectory files from three replicates of Molecular Dynamics simulations.
Provided MMGBSA calculation results and supporting files for each MD run.
Included visual representations of protein backbone RMSD and ligand RMSD, along with hydrogen bond interactions.
The dataset contains over 200 files including trajectory and MMGBSA results.
Significant ligand interactions with catalytic dyads are documented, supporting BACE1 inhibition discovery.
Visual aids illustrate RMSD and hydrogen bond occupancy trends across different simulation replicates.

Abstract

The complete dataset of all three replicates of the Molecular Dynamics Simulation and MM/GBSA Estimation of Compound 41. Supplemental Material to the research "Integrating Structure-Based Genetic Algorithms and Deep Reinforcement Learning for the De Novo Discovery of Novel BACE1 Inhibitors". This compressed folder includes: + Raw and processed Molecular Dynamics trajectory files of each replicate in corresponding folders (e. g. meᵣep1. xtc (raw MD trajectory) ; centered. xtc (centered file) ; mdₚrocessed (processed XTC file) ) + All supporting files of each MD runs (TPR files, MDP files, GRO files, CPT files, TOP files, ITP files) + XVG files and PNG images of each replicate's Protein backbone RMSD and Ligand RMSD + MMGBSA. IN file specifying input of MMGBSA calculations + MMGBSA calculation results (COMPACTMMXSARESULTS. mmxsa; FINALDECOMPMMPBSA. dat; FINALRESULTSMMPBSA. dat) and log files + MMGBSA summary files (CLEANFINALDECOMPMMPBSA. csv) + VMD's hydrogen bonds occupancies processed files and images: hbonds. dat, hbonds-details. dat, and 41ᵣep*dyad. png provide information on ligand's hydrogen bond interactions with the catalytic dyad, and hbondsₚrotein. dat, hbonds-detailsₚrotein. dat, and 41ₚroteinᵣep*. png provide information on ligand's hydrogen bond interactions with any residuals

Dataset of Molecular Dynamics Simulation and MM/GBSA Calculation of Compound 41

Key Points

Abstract

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