SpringSaLaD software

SpringSaLaD software is built with a GUI supporting model creation, running simulations, and data collection. It is available for download for Mac, Unix, and Windows platforms.

SpringSaLaD is:

• a particle-based, spatial stochastic simulator for molecules in 3D molecules presented as a collection of impenetrable spheres (called “sites”) in 3D linked by stiff springs.
• The sites represent protein binding domains, such as an SH2 domain or a catalytic domain, each site can be associated with a number of biochemical states, such as “active” or “inactive” for a catalytic domain.
• each site has a separate diffusion
• binding among sites is represented as a formation of a new spring between sites
• supports particle creation, particle decay, association and dissociation, and state transitions.

SpringSaLaD is most suitable for modeling mesoscopic systems, which are far too large to be modeled with molecular dynamics but which require more detail than obtainable with macroscopic continuum models. A good example of a system which is best modeled with SpringSaLaD is ligand-mediated receptor clustering, where coarse-grained particle-level interactions are required but atom-level information is not of interest. In general, SpringSaLaD is best used to model mesoscopic particles (diameters of 1 – 10 nm, which could represent a functional protein domain), moderately sized systems (10 – 10,000 particles), and times scales on the order of 1 second, but no actual restriction is set on size or scale of the simulated system.