Proteins have the ability to assemble in multimeric states to perform their specific biological function. Unfortunately, characterizing experimentally these structures at atomistic resolution is usually difficult. For this reason, in silico methodologies aiming at predicting how multiple protein copies arrange to forma multimeric complex would be desirable. We present Parallel OptimizationWorkbench (POW), a swarm intelligence based optimization framework able to deal, in principle, with any optimization problem. We show that POW can be applied to biologically relevant problems such as prediction of protein assemblies and the parameterization of a Coarse-Grained force field for proteins. By combining POW optimizations, Molecular Dynamics simulations, Poisson-Boltzmann calculations and a variety of experiments, we subsequently study two bacterial nanomachieries: Aeromonas hydrophila's pore-forming toxin aerolysin, and Yersinia enterocolitica injectisome. These structures are challenging both for their size, and for the timescales involved in their functioning. Aerolysin is a pore-forming toxin secreted as an hydrophilic monomer. By means of large conformational changes, the protein heptamerizes on the target cell's surface, and finally inserts β-barrel into its lipid bilayer, causing cell death. The main hurdle in the study of this structure is the complexity of the mode of action, which spans timescales currently unreachable by classical molecular dynamics. We show that aerolysin C-terminal region has the dual role of preventing premature oligomerization and helping the folding of tertiary structure, qualifying therefore as an intramolecular chaperone. We study the transmembrane β-barrel properties and compare them with those of the homologous protein α-hemolysin. We show that aerolysin's barrel is more rigid than α-hemolysin's, and should be anion selective. We present models for aerolysin heptamer both in prepore and, for the first time, in membrane-inserted conformation. Our results are validated experimentally, and are consistent with known biochemical and structural data. The injectisome is an example of a type III secretion system. Its most striking feature is probably its size: hundreds of proteins assemble in a unique structure spanning the Gram-negative bacterial double membrane, and protruding outside the cell as a needle for tenth of nanometers. Obtaining an atomistic representation of this massive structure, and therefore some insights about its mode of action, is one of the greatest challenges. We show that the final length of injectisome's needle is determined by the secondary structure content of a ruler protein located inside its cavity during assembly. Using POW, we also produce the first model for Yersinia injectisome's basal body, highlighting the flexibility of this region in adapting between the inner and outer membranes. As a whole, this work demonstrates that a synergy of dry and wet experiments can provide precious insights into macromolecular structure and function.