Matthews coefficient

The values used for the 1JC4 example are based on the sequence information that there are seven methionines per chain and that the Matthews coefficient and soivent fraction are consistent with four chains in the asymmetric unit therefore,... 

Kantardjieff KA, Rupp B. Matthews coefficient probabilities improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci. 2003 12 1865-1871. 

The Matthews coefficient C attempts to eliminate bias caused by an uneven distribution of cases among categories (i.e., for the two-category case, other than 50% of total cases belonging to each category). It is defined as follows ... 

Matthews coefficient, Z-value, cell transformation matrices Validity of noncrystallographic symmetry Discrepancies with sequence databases Generated automatically or visually checked Identification, geometry, and nomenclature Solvent molecules outside the hydration sphere, syntax checks, internal data consistency checks... 

Matthews and Riley [99] preconcentrated iodide by co-precipitation with chloride ions. This is achieved by adding 0.23 g silver nitrate per 500 ml of seawater sample. Treatment of the precipitate with aqueous bromine and ultrasonic agitation promote recovery of iodide as iodate which is caused to react with excess iodide under acid conditions, yielding I3. This is determined either spectrophotometrically or by photometric titration with sodium thiosulfate. Photometric titration gave a recovery of 99.0 0.4% and a coefficient of variation of 0.4% compared with 98.5 0.6% and 0.8%, respectively, for the spectrophotometric procedure. 

Parameters Controlling Absorption. The absorption of a chemical into the skin is a function of the nature of the molecule, the behavior of the vehicle, and the status of the skin. Three major variables account for differences in the rate of absorption or flux of different topical chemicals or of the same molecule in different vehicles the concentration of the molecule in the vehicle, the partition coefficient of chemical between the stratum comeum and the vehicle, and the diffusion coefficient of molecule in the stratum comeum (Garner and Matthews, 1998). 

Matthews, M.A. and Akgerman, A. Infinite dilution diffusion coefficients of methanol and 2-propanol in water. J. Chem. Eng. Data, 33(2) 122-123, 1988. 

Diffusion coefficients derived from pulsed gradient spin echo NMR-studies show lower values for the encapsulated guest identical to those of the host, see Frish, L. Matthews, S. E. Bohmer, V. Cohen, Y. J. Chem. Soc., Perkin Trans. 2 1999, 669-671. 

Matthews correlation index = Pearson similarity coefficient —> classification parameters > maximal binding energy —> scoring functions (0 average binding energy)... 

Similarity coefficients for binary variables are also used as —> classification parameters for two-dass problems among these, the most used is the Pearson coeffident (Table S9), which is also known as Matthews correlation index. 

My own criterion for evaluating charge density results is to compare the electrostatic physical properties with other experiments.28 1 tried to work up the numbers reported by Matthews et al.21 for a permanent dipole moment, but the information is insufficient since the local atomic axes are not reported. A coordinate system, defined with respect to the unit cell axes, should be supplied moreover, it is convenient for the reader if all population coefficients are rotated into this defined system. Of course, if rotational invariance is violated in the representation, then there is no sense to any of the results. I was also interested in determining the local electric field gradients on the N atoms of the tetracyano-ethylene oxide molecule, but the authors have prejudged the result by arbitrarily setting three of the five local quadrupole terms to zero. 

SUBSTRUCT prediction CNS-, and all molecules with a score >0.5 are classified as CNS-i-. The correlation coefficient (CC) according to Matthews [55] multiplied by 100, and the prediction accuracy (PA) for compounds within specific scoring interval is included. The SUBSTRUCT classification (right) is analogous to the ANN classification [40]. 

A principal component analysis (PCA) using simple molecular descriptors showed that the training and test sets overlapped. Focusing on compounds with a Tanimoto similarity greater than 0.7 resulted in a test set of 28 compounds, which had Matthews correlation coefficient and concordance statistics that... 

The ceric sulfate dosimeter is sensitive to impurities, but this effect can be decreased by the addition of scavengers, e.g., cerous ions, or by preirradiation of the solution to a dose of approximately 1 kGy. Other unfavorable characteristics of the solution are its light sensitivity, energy dependence below 0.1 MeV, dose rate dependence above 10 Gy s and the need to dilute the irradiated solutions for the spectrophotometric evaluation. The temperature coefficient of the solution during irradiation is not significant in the range of 10-62°C (Matthews 1982). 

Bockris, Khan, and Matthews pointed out that if one plots the value of calculated on the solvent fluctuation theory for a number of redox reactions in solution, against the corresponding value, calculated from experiment, with the transmission coefficient assumed to be unity, one obtains no correlation, except that the values theoretically predicted are generally below those observed experimentally. 

In this work, Molecular Dynamics (MD) simulations were performed in order to calculate the diffusion coefficient of H2, CO and H2O in various -alkanes, namely from n-Cs up to n-Cge, at high temperature and pressure conditions. Moreover, the diffusion of the same light components was also examined in binary -Ci2 - n-Cgs mixtures with various compositions as well as in more realistic five- or six- -alkane component mixtures. For -alkanes, an accurate united atom (UA) force field was used (Martin et al. 1998) [12]. H2 and CO were modelled as Leimard-Jones spheres (Hirschfelder et al. 1954) [9] whereas for H2O the popular Extended Simplified Point Charge (SPC/E) model was used (Berendsen et al. 1987) [3]. Limited experimental data (Rodden et al. 1988a, Rodden et al. 1988b and Matthews et al. 1987) [17] [18] [13] for the diffusion coefficient of the light components in n-Cn, -Ci6, -C2o and -C2s were used for the evaluation of simulation results. 

Molecular simulation using realistic force fields provides a reliable prediction of diffusion coefficient (D). However, it is computationally expensive and cannot be used for routine engineering calculations. An alternative approach is to develop phenomenological correlations that represent accurately experimental or molecular simulation data and can be interpolated or even extrapolated in other range of conditions. In the past, many empirical correlations have been developed with varying degree of success (Wilke and Chang (1955), Leahy-Dios and Firoozabadi (2007), Matthews et al. (1987) and Erkey et al. (1990)) [10] [13] [6]. 

In Figure 3a, experimental data (Rodden et al. (1988a) and Matthews et al. (1987)) [17] [ 13] and NVT MD predietions for the self-diffusion coefficient of the three solutes in all -alkanes at 473 K are shown for eomparison. To decrease the imcertainty in calculations, four initially different struetures of each -alkane system were examined. The statistical error reported in the simulations is the standard deviation in the calculated values for the different struetures. D experimental values for H2 and CO in n-Cn, -Ci6, n-Qo and -C28 at 473 K were obtained by interpolation of the experimental data proposed by (Matthews et al., 1987) [13], (Rodden et al., 1988a) [17]... 

The knowledge of the diffusion coefficient is crucial for the proper design of many important industrial processes. (Matthews and Akgerman, 1987) [13] and (Erkey et al., 1990) [6] developed an empirical correlation for predicting the diffusion coefficients of gases and liquid solutes in normal alkanes. The functional form of the correlation is... 

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