基于空间规则的模拟：SRSim软件

Spatial Rule-Based Simulations: The SRSim Software.

作者信息

Henze Richard, Grünert Gerd, Ibrahim Bashar, Dittrich Peter

机构信息

Department of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.

Chair of Bioinformatics, Matthias-Schleiden-Institute, Friedrich Schiller University Jena, Jena, Germany.

出版信息

Methods Mol Biol. 2019;1945:231-249. doi: 10.1007/978-1-4939-9102-0_10.

DOI:10.1007/978-1-4939-9102-0_10

PMID:30945249

Abstract

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.

摘要

SRSim将基于规则的反应网络模型与空间粒子模拟相结合，能够模拟根据一组化学反应规则变化的大分子复合物的动力学。由于规则可以包含分子复合物的模式和某些结合位点的特定状态，因此可以定义组合复杂甚至无限大小的反应网络。粒子根据LAMMPS实现的分子动力学在三维空间中移动，同时使用BioNetGen语言来制定反应规则。几何信息以特定的XML格式添加。通过两种不同的聚合变体以及DNA螺旋形成的玩具模型对模拟协议进行了举例说明。SRSim是开源的，可供下载。