EASAL (Efficient Atlasing, Analysis and Search of Molecular Assembly Landscapes).

To elucidate the structure of assembly configuration spaces, the EASAL software combines classical concepts, such as stratifications of semialgebraic sets, with recent algorithms for efficiently realizing geometric constraint systems, and theoretical advances concerning convex parametrization: in contrast to folding configuration spaces, most regions of assembly and packing configurations admit a convex parametrization. This allows for a novel, efficient and intuitive representation of configuration spaces so that the corresponding atlas can be efficiently generated and sampled. This paper describes the approach, theory, structure and algorithms underlying EASAL and outlines its use for generating atlases of dimeric assemblies of the AAV2 coat protein, and alpha helix packing in transmembrane proteins.