DEMO (Domain Enhanced MOdeling) is a method for automated assembly of
full-length structural models of multi-domain proteins.
Starting from individual domain structures, DEMO first
identify quaternary structure templates that have similar
component domains by domain-level structural alignments
Replica-exchange Monte Carlo simulations are then used to
assemble full-length models, as guided by the
inter-domain distance profiles collected from the
top-ranked quaternary templates.
The final models with the lowest energy are selected from
Monte Carlo trajectories, followed by atomic-level refinments using
fragment-guided molecular dynamics simulations.
DEMO can be used to assemble domains from either
experimental or predicted models for proteins with both
continuous and discontinuous domain architectures.
DEMO On-line Server
[View example of output for
Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang, and Yang Zhang.
Assembling multidomain protein structures through analogous global structural alignments.
Proceedings of the National Academy of Sciences, 116: 15930-15938 (2019). [PDF] [Support Information]