Journal of Computer-Aided Molecular Design

, Volume 32, Issue 1, pp 225–230 | Cite as

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

  • Dzmitry Padhorny
  • David R. HallEmail author
  • Hanieh Mirzaei
  • Artem B. Mamonov
  • Mohammad Moghadasi
  • Andrey Alekseenko
  • Dmitri BeglovEmail author
  • Dima KozakovEmail author


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.


Drug design data resource D3R FFT sampling Protein ligand docking 



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


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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  1. 1.Department of Applied Mathematics and StatisticsStony Brook UniversityStony BrookUSA
  2. 2.Laufer Center for Physical and Quantitative BiologyStony Brook UniversityStony BrookUSA
  3. 3.Acpharis Inc.HollistonUSA
  4. 4.Department of Biomedical EngineeringBoston UniversityBostonUSA
  5. 5.Moscow Institute of Physics and Technology (State University)Dolgoprudny, Moscow OblastRussia
  6. 6.Institute of Computer Aided Design of the Russian Academy of SciencesMoscowRussia

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