Conformation sampling distance geometry

Conformational Sampling Distance Geometry Theory, Algorithms, and Chemical Applications Macromolecular Structure Calculation and Refinement by Simulated Annealing Methods and Applications NMR Chemical Shift Computation Structural Applications NMR Refinement. 

Metzler W J, Hare D R and Pardi A 1989 Limited sampling of conformational space by the distance geometry algorithm implications for structures generated from NMR data Bioohemistry 2S 7045-52... 

Note that although the bounds on the distances satisfy the triangle inequalities, particular choices of distances between these bounds will in general violate them. Therefore, if all distances are chosen within their bounds independently of each other (the method that is used in most applications of distance geometry for NMR strucmre determination), the final distance matrix will contain many violations of the triangle inequalities. The main consequence is a very limited sampling of the conformational space of the embedded structures for very sparse data sets [48,50,51] despite the intrinsic randomness of the tech-... 

Havel, T. F. The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide-chains a smdy of 1830 independently computed conformations. Biopolymers 1990, 29,1565-1585. 

W. J. Metzler, D. R. Hare, and A. Pardi, Biochemistry, 28,7045, (1989). Limited Sampling of Conformational Space by the Distance Geometry Algorithm Implications for Structures Generated from NMR Data. 

T. F. Havel, Biopolymers, 29, 1565 (1990). The Sampling Properties of Some Distance Geometry Algorithms Applied to Unconstrained Polypeptide Chains A Study of 1830 Independently Computed Conformations. 

Fig. 2. Schematic representation of conformational space exploration efficiencies and their dependency for the different sampling scale with, insufficient (A), nearly sufficient (B), and almost sufficient (C) number of initial structures. In this example, preliminary calculations are distance geometry or torsion angle space algorithms, and refinement is restraint molecular dynamics with same set of NMR-derived structural information. The exploration extents of the refinements are assumed to be similar for selected preliminary calculation s results (i.e., initial structures of the refinement calculations).

Distance Geometry Algorithm for Conformational Sampling of Cyclic Structures. 

Geometry optimization of the proposed mimetic is included as part of the design analysis to ensure the feasibility of the desired molecular conformation. MM and semiempirical quantum mechanical methods have been used most extensively for these purposes. Conformational analysis of the proposed mimetic allows the determination of an energy profile for the molecule under consideration. This has been used by researchers to assess where the desired conformation for the mimetic resides on the molecular potential energy surface. Monte Carlo, MD, and distance geometry-based conformational search techniques have been employed extensively to sample conformational space. Computational methods that attempt to approximate the efifects of aqueous solvation on the conformational profile of the mimetic are being used more frequently as part of these efforts. 

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