Fig. 1: Overview of the analysis procedure.
From: A computational toolbox for the assembly yield of complex and heterogeneous structures
We depict the process by which we predict assembly yield as a functions of system parameters, using the TRAP protein complex as an example. Starting with a given complex (here, a PDB file), we generate a coarse-grained model (here, each amino acid is replaced by a sphere). We specify the contacts at the various binding interfaces and their strengths (here, using patches at the interfaces). We then enumerate all possible structures that can form (in this case, 3 monomers, 3 dimers, 1 trimer). Finally, we compute the partition function for each structure as described in this work, and compute the expected yields of each structure as a function of system parameters. The true yield curves for the TRAP protein complex are shown in Fig. 4.
