DESSA is a simulator of self-assembly processes that generates stochastic samples among possible assembly trajectories of a coarse-grained model of molecular assembly. Models are specified using simple “local rules” that describe allowed binding interactions and associated kinetic rates for an assembly model. DESSA uses a variant of the stochastic simulation algorithm (SSA) adapted for more efficient run time and memory usage on systems with large numbers of assembly intermediates. The primary application of DESSA is virus capsid assembly.

Example visualization of a simulated virus capsid assembly process for human papillomavirus.