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A program for the computation of helical parameters from internal coordinates

S Colombano, R Rein, R D MacElroy

    Computer Programs in Biomedicine
    |February 1, 1980
    PubMed
    Summary
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    A new FORTRAN IV program calculates helical parameters and atomic coordinates from internal coordinates. This method aids in systematically studying protein-DNA recognition.

    Area of Science:

    • Structural biology
    • Computational chemistry
    • Bioinformatics

    Background:

    • Understanding the helical parameters of molecular structures is crucial for analyzing their function.
    • Protein-DNA recognition involves complex interactions influenced by the helical geometry of both molecules.

    Purpose of the Study:

    • To implement a computational method for calculating helical parameters from internal coordinates.
    • To obtain atomic coordinates in a cylindrical system.
    • To apply this method to protein-DNA recognition.

    Main Methods:

    • A FORTRAN IV program was developed to calculate helical parameters.
    • The program utilizes internal coordinates of arbitrary repeat units.
    • Atomic coordinates are generated in a cylindrical coordinate system.

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    Main Results:

    • A functional program capable of calculating helical parameters and atomic coordinates was created.
    • The program provides a systematic approach for analyzing molecular structures.

    Conclusions:

    • The developed method and program offer a valuable tool for structural analysis.
    • This approach facilitates a systematic investigation into protein-DNA recognition mechanisms.