Potential conformers probability assessment

A method called PARSE (Probability Assessment via Relaxation rates of a Structural Ensemble) is described for determination of ensembles of structures from NMR data. The problem is approached in two separate steps (1) generation of a pool of potential conformers, and (2) determination of the conformers probabilities which best account for the experimental data. The probabilities are calculated by a global constrained optimization of a quadratic objective function measuring the agreement between observed NMR parameters and those calculated for the ensemble. The performance of the method is tested on synthetic data sets simulated for various structural ensembles of the complementary dinucleotide d(CA) d(TG). 

ULYANOV ETAL. Conformational Sampling and Probability Assessment 185 Probability Assessment of Potential Conformers... 

Nevertheless, the ability to constrain dihedral angles can be useful in simulations in which one needs to assess the behavior of a molecule as a function of conformation. An important application of this type of constraint is the evaluation of potentials of mean force (PMF), which provide the work required to move the system along a predefined dihedral coordinate. The thermal probability is directly related to this free energy profile. PMF provide a means of estimating relative stabilities of conformers as well as the kinetics of conformational changes. 

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