NMR Refinement (NOE, CS, RDC)
This method calculates highly accurate protein structures from input sequence and sparse NMR data. Without NMR data, such structures would be impossible to calculate or have much lower accuracy. This is a variant on the Rosetta ab initio method specifically modified to: a) Adjust backbone torsion angles such that they obey Chemical Shift data (CS), and b) to constrain Rosetta structure prediction based on NOE NMR Experiments (Nuclear Overhauser Effect) and/or RDC data.
Raman S, et al Science 2010 Sgourakis NG et al JACS, 2011, 133(16):6288-98:
This method uses Rosetta and X-Ray structure data handling tools to automatically refine a starting model (e.g., from molecular replacement with a homologous structure) into X-Ray crystallographic density. It iterates toward a final structure through repeatedly iterating pairs of calculations: A) homology modeling including restraints to the experimentally-derived density map; B) density map re-calculation based on the current homology model. These pairs of calculations are repeated until convergence is achieved. The result is a high quality refined model that is often significantly better than the model that could be determined using standard X-Ray refinement approaches. This process can save months of time and can potentially identify better final structures than a human modeler. DiMaio et al “Improved protein crystal structures at low resolution by integrated refinement with Phenix and Rosetta.”
Nature Methods. 10:1102-4. (2013)