Improving the binding affinity estimations of protein–ligand complexes using machine-learning facilitated force field method

Abstract

Scoring functions are routinely deployed in structure-based drug design to quantify the potential for protein–ligand (PL) complex formation. Here, we present a new scoring function Bappl+ that is designed to predict the binding affinities of non-metallo and metallo PL complexes. Bappl+ outperforms other state-of-the-art scoring functions, achieving a high Pearson correlation coefficient of up to ~ 0.76 with low standard deviations. The biggest contributors to the increased performance are the use of a machine-learning model and the enlarged training dataset. We have also evaluated the performance of Bappl+ on target-specific proteins, which highlighted the limitations of our function and provides a way for further improvements. We believe that Bappl+ methodology could prove valuable in ranking candidate molecules against a target metallo or non-metallo protein by reliably predicting their binding affinities, thus helping in the drug discovery process.

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Acknowledgements

Authors gratefully acknowledge support to SCFBio from the Department of Biotechnology, Govt. of India. The authors thank Dr. Prashant S. Rana for sharing his insights into the random forest and Mr. Manpreet Singh for web-enabling Bappl+.

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AS, BJ conceived the project. AS performed all the calculations. RB helped in fine-tuning the work and in generating the web server. All authors analyzed the data and wrote the manuscript.

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Correspondence to B. Jayaram.

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Soni, A., Bhat, R. & Jayaram, B. Improving the binding affinity estimations of protein–ligand complexes using machine-learning facilitated force field method. J Comput Aided Mol Des 34, 817–830 (2020). https://doi.org/10.1007/s10822-020-00305-1

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Keywords

  • Protein–ligand interactions
  • Binding affinity
  • Scoring functions
  • Random forest