PARSE parameter set

The solvent dielectric constant, ionic strength and temperature are chosen to fit the conditions of the experimental studies. The protein dielectric constant is assigned some small value, e.g. 4. The PB calculations are currently carried out with the atomic charges and radii of the PARSE parameter set, developed by Honig and coworkers [17] or that for CHARMM [12]. The PARSE parameter set... 

At this point it seems useful to explain the PARSE charges mentioned above. The assignment of charges in the PARSE parameter set was based on the following procedure ... 

To parse a sentence completely by a rule, the second parameter has to be set to the empty list ... 

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). 

The JCAMP-DX file is divided into the sections CORE and NOTES. The intention is to separate the essential information to be parsed by the computer from the associated noncritical support data. The CORE can be regarded as the irreducible minimum content of a JCAMP-DX file. The CORE is split into two sections, the CORE HEADER and the CORE DATA. In between these two sections are the LDRs belonging to the NOTES. A JCAMP-DX file has all of the textual information and parameters defining the data set at the top of the data file and the numerical data block follows at the end (Figure 1). 

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