Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs.Xu, Y., Wu, J., Gorenstein, D., Braun, W.
(1999) J.Magn.Reson. 136: 76-85
- PubMed: 9887292
- DOI: 10.1006/jmre.1998.1616
- PubMed Abstract:
- Automated Assignment of Simulated, Experimental Noesy Spectra of Proteins by Feedback Filtering and Self-Correcting Distance Geometry
Mumenthaler, C.,Braun, W.
(1995) J.Mol.Biol. 254: 465
- Exact and Efficient Analytical Calculation of the Accessible Surface Areas and Their Gradients Macromolecules
Fraczkiewicz, R.,Braun, W.
(1998) J.Comput.Chem. 19: 319
- Automated Combined Assignment of Noesy Spectra and Three-Dimensional Protein Structure Determination
Mumenthaler, C.,Guntert, P.,Braun, W.,Wuthrich, K.
(1997) J.Biomol.NMR 10: 351
- A Program, Fantom, for Energy Refinement of Polypeptides and Proteins Using a Newton-Raphson Minimizer in the Torsion Angle Space
Schaumann, T.H.,Braun, W.,Wuthrich, K.
(1990) Biopolymers 29: 679
- Combined Automated Assignment of NMR Spectra and Calculation of Three- Dimensional Protein Structures
Xu, Y.,Schein, C.H.,Braun, W.
(1999) Biological Magnetic Resonance 17: 37
The NOAH/DIAMOD program suite was used to automatically assign an experimental 2D NOESY spectrum of the 46 residue protein crambin(S22/I25), using feedback filtering and self-correcting distance geometry (SECODG). Automatically picked NOESY cross pea ...
The NOAH/DIAMOD program suite was used to automatically assign an experimental 2D NOESY spectrum of the 46 residue protein crambin(S22/I25), using feedback filtering and self-correcting distance geometry (SECODG). Automatically picked NOESY cross peaks were combined with 157 manually assigned peaks to start NOAH/DIAMOD calculations. At each cycle, DIAMOD was used to calculate an ensemble of 40 structures from these NOE distance constraints and random starting structures. The 10 structures with smallest target function values were analyzed by the structure-based filter, NOAH, and a new set of possible assignments was automatically generated based on chemical shifts and distance constraints violations. After 60 iterations and final energy minimization, the 10 structures with smallest target functions converged to 1.48 A for backbone atoms. Despite several missing chemical shifts, 426 of 613 NOE peaks were unambiguously assigned; 59 peaks were ambiguously assigned. The remaining 128 peaks picked automatically by FELIX are probably primarily noise peaks, with a few real peaks that were not assigned by NOAH due to the incomplete proton chemical shifts list.
Sealy Center for Structural Biology and Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas, 77555-1157, USA.