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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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    This study introduces an internal frame of reference (IFR) for molecular analysis. This method enables consistent spatial distribution function (SDF) calculations for molecular trajectories and ensembles.

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    Area of Science:

    • Molecular dynamics
    • Computational chemistry
    • Structural biology

    Background:

    • Spatial distribution functions (SDFs) are crucial for understanding molecular structure and dynamics.
    • Accurate SDF computation requires a stable molecular reference frame.
    • Existing methods lack a consistent approach for tracking molecular structures over time.

    Purpose of the Study:

    • To introduce a novel concept of an internal frame of reference (IFR) for molecular structures.
    • To develop an algorithm for tracking the IFR in molecular trajectories and ensembles.
    • To enable consistent and meaningful SDF calculations for molecular systems.

    Main Methods:

    • Developed the internal frame of reference (IFR) concept for labeled point sets.
    • Proposed a variant of Kabsch's algorithm for tracking the IFR over time and space.
    • Applied the IFR method to generate consistent SDFs for molecular data.

    Main Results:

    • Successfully tracked IFR for molecular trajectories and ensembles.
    • Demonstrated consistent SDF aggregation using the IFR approach.
    • Validated the technique with docking scenarios involving DNA, insulin, and aspirin.

    Conclusions:

    • The IFR method provides a robust framework for molecular spatial analysis.
    • This approach enhances the reliability of SDF calculations in molecular simulations.
    • The technique is broadly applicable to various molecular systems and datasets.