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Journal of Computer-Aided Molecular Design

, Volume 32, Issue 2, pp 363–374 | Cite as

Congestion game scheduling for virtual drug screening optimization

  • Natalia Nikitina
  • Evgeny Ivashko
  • Andrei Tchernykh
Article

Abstract

In virtual drug screening, the chemical diversity of hits is an important factor, along with their predicted activity. Moreover, interim results are of interest for directing the further research, and their diversity is also desirable. In this paper, we consider a problem of obtaining a diverse set of virtual screening hits in a short time. To this end, we propose a mathematical model of task scheduling for virtual drug screening in high-performance computational systems as a congestion game between computational nodes to find the equilibrium solutions for best balancing the number of interim hits with their chemical diversity. The model considers the heterogeneous environment with workload uncertainty, processing time uncertainty, and limited knowledge about the input dataset structure. We perform computational experiments and evaluate the performance of the developed approach considering organic molecules database GDB-9. The used set of molecules is rich enough to demonstrate the feasibility and practicability of proposed solutions. We compare the algorithm with two known heuristics used in practice and observe that game-based scheduling outperforms them by the hit discovery rate and chemical diversity at earlier steps. Based on these results, we use a social utility metric for assessing the efficiency of our equilibrium solutions and show that they reach greatest values.

Keywords

Drug discovery Virtual drug screening High-performance computing High-throughput computing Desktop grid Game theory Congestion game 

Notes

Acknowledgements

This work is partially supported by the Russian Fund for Basic Research under Grant Nos. 16-07-00622, 15-29-07974 and 16-51-55006, and CONACYT (Consejo Nacional de Ciencia y Tecnología, México) under Grant No. 178415.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Institute of Applied Mathematical Research, Karelian Research CenterRussian Academy of SciencesPetrozavodskRussia
  2. 2.Computer Science DepartmentCICESE Research CenterEnsenadaMexico

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