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Users Guide and Tutorial SpringSaLaD.jar

 

SpringSaLaD, (PubMed) is a particle-based, stochastic, biochemical simulation platform 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. In SpringSaLaD, molecules are modeled as a collection of impenetrable spheres (called “sites”) linked by stiff springs. The sites are intended to represent mesoscopic protein domains, such as an SH2 domain or a catalytic domain, and each site can be associated with a number of biochemical states, such as “active” or “inactive” for a catalytic domain. SpringSaLaD supports the full array of typical biochemical reactions: zeroeth-order reactions which model particle creation, a variety of first-order reactions such as particle decay, dissociation, and state transitions, and second-order reactions between sites for bonding reactions.

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.

SpringSaLaD is available as JAR file. It includes a user-friendly GUI which supports all aspects of model creation, running simulations, and data analysis.

The source code for SpringSaLaD is freely available at GitHub.

Release Notes

In Version 2, released Nov. 29, 2017, the primary new feature is the ability to directly build models from atomic coordinates in pdb files. As illustrated here, this also includes an interactive 3D viewer that allows the user to directly compare the PDB structures to the coarse-grained linked spheres representation used in SpringSaLaD. Improvements to the organization of SpringSaLaD project files have also been made.