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ArbAlign: A Tool for Optimal Alignment of Arbitrarily Ordered Isomers Using the Kuhn-Munkres Algorithm.

Berhane Temelso1, Joel M Mabey1, Toshiro Kubota2

  • 1Dean's Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University , Lewisburg, Pennsylvania 17837, United States.

Journal of Chemical Information and Modeling
|April 12, 2017
PubMed
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This study introduces a faster method for comparing molecular structures by using the Kuhn-Munkres algorithm. This approach efficiently finds the optimal atom ordering for accurate root-mean-square distance calculations.

Area of Science:

  • Computational chemistry
  • Structural bioinformatics

Background:

  • Calculating molecular similarity often requires aligning structures using root-mean-square distance (RMSD).
  • Standard RMSD calculations assume identical atom ordering and molecular axes, which is not always the case for isomers or differently represented molecules.

Purpose of the Study:

  • To develop an efficient algorithm for determining the optimal atom ordering and molecular axes alignment for pairwise RMSD calculations.
  • To overcome the computational limitations of factorial scaling for comparing molecular structures with differing atom orders.

Main Methods:

  • Utilized the Kuhn-Munkres matching algorithm to find the optimal atom ordering.
  • Reduced the computational complexity of finding the best atom ordering from factorial to polynomial scaling.

Related Experiment Videos

  • Validated the method on various molecular clusters and rigid systems.

    • Main Results:

    • The Kuhn-Munkres algorithm significantly reduces the computational cost of finding optimal molecular alignments.
    • The method enables efficient and accurate RMSD calculations for molecules with different atom orderings.
    • The developed tool is available as a standalone application and an online web server.

    Conclusions:

    • The Kuhn-Munkres algorithm provides an efficient solution for the computationally intensive problem of optimal molecular structure alignment.
    • This approach facilitates more accurate and accessible molecular similarity assessments in computational chemistry and related fields.
    • The freely available tool and web server promote wider adoption and application of this improved methodology.