Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations

@article{Nilges1988DeterminationOT,
  title={Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations},
  author={Michael Nilges and G. Marius Clore and Angela M. Gronenborn},
  journal={FEBS Letters},
  year={1988},
  volume={229}
}
Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties
TLDR
A protocol for distance geometry calculation is shown to have excellent sampling properties in the determination of three-dimensional structures of proteins from nuclear magnetic resonance (NMR) data and the intrinsic nature of the structures generated with distance restraints derived from NMR data has been revealed.
NMR structure calculation methods for large proteins Application of torsion angle dynamics and distance geometry/simulated annealing to the 269-residue protein serine protease PB92
Molecular dynamics in torsion angle space together with the well established combination of metric matrix distance geometry and simulated annealing in Cartesian space have been applied to the
Three-dimensional structure of acyl carrier protein in solution determined by nuclear magnetic resonance and the combined use of dynamical simulated annealing and distance geometry.
The solution conformation of acyl carrier protein from Escherichia coli (77 residues) has been determined on the basis of 423 interproton-distance restraints and 32 hydrogen-bonding restraints
Limited sampling of conformational space by the distance geometry algorithm: implications for structures generated from NMR data.
TLDR
Calculations with a metric matrix distance geometry algorithm were performed that show that the standard implementation of the algorithm generally samples a very limited region of conformational space and has a tendency to consistently produce similar structures instead of sampling all structures consistent with the input distance information.
Structural refinement by restrained molecular‐dynamics algorithm with small‐angle X‐ray scattering constraints for a biomolecule
A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared
Genfold: A genetic algorithm for folding protein structures using NMR restraints
We report the development and validation of the program GENFOLD, a genetic algorithm that calculates protein structures using restraints obtained from NMR, such as distances derived from nuclear
Comparison of the accuracy of protein solution structures derived from conventional and network‐edited NOESY data
TLDR
Two network‐editing approaches were applied as three‐dimensional, heteronuclear‐edited experiments to distance measurement in a small protein, turkey ovomucoid third domain (OMTKY3), and the resulting two families of structures were found to differ significantly.
Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space
A method is introduced to represent an ensemble of conformers of a protein by a single structure in torsion angle space that lies closest to the averaged Cartesian coordinates while maintaining
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints
TLDR
Dynamical annealing calculations show that loosened internuclear constraints can allow molecules to overcome local minima in the search for a global minimum with respect to both the NMR‐derived constraints and conformational energy.
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Model calculations are performed to evaluate the utility of molecular dynamics with NMR interproton distance restraints for determining the three-dimensional structure of proteins and it is shown that a restrained dynamics structure with significantly larger deviations can be characterized as incorrect, independent of a knowledge of the crystal structure.
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