Protein–ligand docking using FFT based sampling: D3R case study

Abstract

Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein–protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein–peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein–ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein–ligand interaction landscape, which will be explored in further applications.

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Acknowledgements

This work was supported by Grants NSF CCF AF 1527292, NIH R43 GM109555, RSF No 14-11-00877.

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Correspondence to David R. Hall or Dmitri Beglov or Dima Kozakov.

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Padhorny, D., Hall, D.R., Mirzaei, H. et al. Protein–ligand docking using FFT based sampling: D3R case study. J Comput Aided Mol Des 32, 225–230 (2018). https://doi.org/10.1007/s10822-017-0069-7

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Keywords

  • Drug design data resource
  • D3R
  • FFT sampling
  • Protein ligand docking