SpringSaLaD: A Spatial, Particle-Based Biochemical Simulation Platform with Excluded Volume.

ABSTRACT: We introduce Springs, Sites, and Langevin Dynamics (SpringSaLaD), a comprehensive software platform for spatial, stochastic, particle-based modeling of biochemical systems. SpringSaLaD models biomolecules in a coarse-grained manner as a group of linked spherical sites with excluded volume. This mesoscopic approach bridges the gap between highly detailed molecular dynamics simulations and the various methods used to study network kinetics and diffusion at the cellular level. SpringSaLaD is a standalone tool that supports model building, simulation, visualization, and data analysis, all through a user-friendly graphical user interface that should make it more accessible than tools built into more comprehensive molecular dynamics infrastructures. Importantly, for bimolecular reactions we deri

SUBMITTER: Michalski PJ 

PROVIDER: S-EPMC4744174 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature