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Pairwise Performance Comparison of Docking Scoring Functions: Computational Approach Using InterCriteria Analysis.

Maria Angelova1, Petko Alov1, Ivanka Tsakovska1

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Summary
This summary is machine-generated.

This study compares molecular docking scoring functions using InterCriteria Analysis (ICrA). The lowest root mean square deviation (RMSD) proved the best docking output, with Alpha HB and London dG showing high comparability.

Keywords:
InterCriteria analysismolecular dockingmolecular operating environmentscoring functions

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Scoring functions are crucial for approximating binding affinity in molecular docking.
  • Accurate scoring functions are essential for identifying potential drug candidates.
  • Evaluating and comparing scoring functions is vital for improving docking protocol reliability.

Purpose of the Study:

  • To perform a pairwise comparison of five scoring functions from Molecular Operating Environment (MOE) software.
  • To assess the performance of scoring functions using a multi-criterion decision-making approach (InterCriteria Analysis - ICrA).
  • To identify the most effective docking outputs and scoring functions for protein-ligand complex analysis.

Main Methods:

  • Utilized InterCriteria Analysis (ICrA) for a multi-criterion decision-making comparison of scoring functions.
  • Evaluated five MOE scoring functions on protein-ligand complexes from the PDBbind database.
  • Analyzed docking outputs including best docking score, lowest RMSD, and RMSD of the best score pose.

Main Results:

  • The lowest root mean square deviation (RMSD) was identified as the best-performing docking output.
  • Alpha HB and London dG scoring functions demonstrated the highest comparability among the evaluated functions.
  • Investigated the impact of ICrA thresholds and performed correlation analysis.

Conclusions:

  • The proposed ICrA approach offers a robust method for comparing molecular docking scoring functions.
  • Lowest RMSD is a reliable metric for evaluating docking pose accuracy.
  • Alpha HB and London dG show promise for enhanced protein-ligand binding affinity prediction.