SPATKIN

SPATKIN is a simulator that uses rule-based modeling to study the dynamics of biomolecular sites on surfaces. It is a two-dimensional, lattice-based algorithm that tracks molecules and stochastically fires reaction events. This network-free approach does not require the complete reaction network to be generated prior to the simulation. SPATKIN can simulate adsorption, desorption, and crowding processes.

Topic

Molecular dynamics;Molecular modelling;Simulation experiment;Molecular interactions, pathways and networks

Detail

  • Operation: Molecular dynamics

  • Software interface: Library

  • Language: C++

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.0.0

  • Credit: Polish National Science Centre (NCN), National Institutes of Health NIH-NIGMS.

  • Input: -

  • Output: -

  • Contact: spatkin.simulator@gmail.com, Prof. Tomasz Lipniacki tlipnia@ippt.pan.pl, Ms. Agnieszka Ponarska aponar@ippt.pan.pl

  • Collection: -

  • Maturity: -

Publications

  • SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.
  • Kochanczyk M, et al. SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces. SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces. 2017; 33:3667-3669. doi: 10.1093/bioinformatics/btx456
  • https://doi.org/10.1093/bioinformatics/btx456
  • PMID: 29036531
  • PMC: PMC5860254

Download and documentation

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