We discuss how to compute structures, assemblies, and thermodynamic properties of beta barrel membrane proteins, as well as discovery of building blocks of this class of protins that might be useful for design of membrane proteins of desired conductance. Based on a model of physical interactions, a discrete state space, and an empirical potential function derived from detailed combinatorial analysis of protein structures, as well as a model to account for inter-strand loop entropy, we discuss prediction of structures of TM-segments and loops, oligomerization states, protein-protein interaction interfaces, transfer free energy scales, folding stability, and protein topological orientation, as well as general stabilization strategies that is applicable for design of stable bionanopore