Spatial Rule-Based Simulations: The SRSim Software

  • Richard Henze
  • Gerd Grünert
  • Bashar Ibrahim
  • Peter DittrichEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1945)


SRSim combines rule-based reaction network models with spatial particle simulations allowing to simulate the dynamics of large molecular complexes changing according to a set of chemical reaction rules. As the rule can contain patterns of molecular complexes and specific states of certain binding sites, a combinatorially complex or even infinitely sized reaction network can be defined. Particles move in a three-dimensional space according to molecular dynamics implemented by LAMMPS, while the BioNetGen language is used to formulate reaction rules. Geometric information is added in a specific XML format. The simulation protocol is exemplified by two different variants of polymerization as well as a toy model of DNA helix formation. SRSim is open source and available for download.

Key words

Modeling Simulation Chemoinformatics Molecular dynamics Polymerization LAMMPS BioNetGen 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Richard Henze
    • 1
  • Gerd Grünert
    • 1
  • Bashar Ibrahim
    • 2
  • Peter Dittrich
    • 1
    Email author
  1. 1.Department of Mathematics and Computer ScienceFriedrich Schiller University JenaJenaGermany
  2. 2.Chair of Bioinformatics, Matthias-Schleiden-InstituteFriedrich Schiller University JenaJenaGermany

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