Figure 10.

Modeling of structures from cross-linking constraints. (a) Conceptual diagram of high-level modular RNA domains that are flexible and dynamic. (b) Clustering of contacts define RNA domains. (c) Divide and then fold approach for secondary structure modeling, exemplified by 3 cross-links. (d) Fold and then cluster approach for secondary structure modeling, for 2 example alternative conformations. (e) Typical fragment assembly-based approach for 3D modeling, where known 3D fragments are assembled and constrained by cross-linking data (e.g., Rosetta).