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Charge Group Partitioning in Biomolecular Simulation

  • Stefan Canzar
  • Mohammed El-Kebir
  • René Pool
  • Khaled Elbassioni
  • Alpesh K. Malde
  • Alan E. Mark
  • Daan P. Geerke
  • Leen Stougie
  • Gunnar W. Klau
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7262)

Abstract

Molecular simulation techniques are increasingly being used to study biomolecular systems at an atomic level. Such simulations rely on empirical force fields to represent the intermolecular interactions. There are many different force fields available|each based on a different set of assumptions and thus requiring different parametrization procedures. Recently, efforts have been made to fully automate the assignment of force-field parameters, including atomic partial charges, for novel molecules. In this work, we focus on a problem arising in the automated parametrization of molecules for use in combination with the gromos family of force fields: namely, the assignment of atoms to charge groups such that for every charge group the sum of the partial charges is ideally equal to its formal charge. In addition, charge groups are required to have size at most k. We show \(\mathcal{NP}\)-hardness and give an exact algorithm capable of solving practical problem instances to provable optimality in a fraction of a second.

Keywords

charge groups atomic force fields gromos biomolecular simulation tree-decomposition dynamic programming 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Stefan Canzar
    • 1
  • Mohammed El-Kebir
    • 1
    • 2
  • René Pool
    • 2
    • 3
  • Khaled Elbassioni
    • 4
  • Alpesh K. Malde
    • 5
  • Alan E. Mark
    • 5
    • 6
  • Daan P. Geerke
    • 3
  • Leen Stougie
    • 1
    • 7
  • Gunnar W. Klau
    • 1
  1. 1.Centrum Wiskunde & InformaticaLife Sciences GroupAmsterdamNetherlands
  2. 2.Centre for Integrative Bioinformatics VUVU UniversityAmsterdamNetherlands
  3. 3.Division of Molecular ToxicologyVU UniversityAmsterdamNetherlands
  4. 4.Max-Planck-Institut für InformatikSaarbrückenGermany
  5. 5.School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneAustralia
  6. 6.Institute for Molecular BioscienceThe University of QueenslandBrisbaneAustralia
  7. 7.Department of Operations ResearchVU UniversityAmsterdamNetherlands

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