Residual dipolar coupling tests

The push to highlight performance on GPUs has meant that not one of the currently published papers on GPU implementations of MD actually provide any validation of the approximations made in terms of statistical mechanical properties. For example, one could include showing that converged simulations run on a GPU and CPU give identical radial distribution functions, order parameters, and residue dipolar couples to name but a few possible tests. 

NMR residual dipolar couplings (RDCs), in the form of the projection angles between the respective internuclear bond vectors, have been used by Haliloglu et as structural restraints in the ab initio structure prediction of a test set of six proteins. The restraints have been applied using a recently developed SICHO (5/de CHain Only) lattice protein model that employs a replica exchange Monte Carlo algorithm to search conformational space. The proteins studied were ACP (77 residues), rubredoxin (53 residues), NSl, a 73 residue RNA binding/dimeriz-ation domain, Nodf (35 residues), Crd (137 residues) and Bret domain with 92 residues. 

Several different structural data subsets including vicinal and residual dipolar couplings measured for oxidized cytochrome bsei have been used to test the speed of the process of structure determination versus structure quality by Band et The authors results indicate that the set of the backbone-only restraints is sufficient to accurately determine 3D fold of the protein. 

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