Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
The upper bounds obtained from MARDIGRAS were multiplied by a factor 1.25 before being exported to Amber 10 for a 25 ps simulated annealing protocol. The simulated annealing protocol using the pairwise generalized Born model was as follows: the temperature of the system was kept constant at 600 K during the first 5 ps, cooled down slowly to 100 K between 5-18 ps, and cooled down to 0 K for the last 7 ps. The protocol was repeated 50 times to obtain an NMR ensemble with the 10 lowest RMSD structures. The structure with the lowest RMSD of the ensemble was put back into MARDIGRAS for a second and third cycle of NOE calibration and structure calculations.
VnmrJ
NMR Ensemble Information
Conformer Selection Criteria
lowest RMSD to average structure
Conformers Calculated Total Number
50
Conformers Submitted Total Number
10
Representative Model
1 (closest to the average)
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
collection
VnmrJ
2.1B
Varian
2
processing
NMRPipe
4.9
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3
chemical shift assignment
NMRView
8.0.b30
Johnson, One Moon Scientific
4
noe calibration
MARDIGRAS
T.L. James
5
structure solution
Amber
10
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
6
refinement
Amber
10
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm