Alignment models

The usual alignment algorithm fixes 0 and A as 0o and Aq, so that the prior is 1 when 0 = 00 and A = Aq and is 0 otherwise. Clearly, if experience justifies this choice or some other nonuniform choice, we can choose an informative prior that biases the calculation to certain values for the parameters or limits them to some likely range. The likelihood is well defined by the alignment model defined by using a similarity matrix and affine gap penalties, so that... 

When this is done, the dependence of k(Ee) upon Ee is even greater than predicted by the dipole-alignment model, and the thermal rate constant predicted from this variation, extrapolated to thermal energies, is more than twice the thermal rate constant found experimentally by using the pulsing technique. 

Table 8.2 Root mean square deviation (RMSD) of the backbone of the aligned models of the h AR. The main difference among the models is due to the loops, which represent the most variable region of the templates and consequently of the models. Particular attention has to be given to EL2 because it is part of the binding pocket and it can directly interact with ligands...

Accession number ] [Gene sequence] Alignment Modelling Secondary structure Figure 14.3 Information about an enzyme (e g., leucine dehydrogenase, LeuDH) in the databases. 

Alignment Colchicine, CA4, allocolchi-cine, 2-methoxy-5-(2, 3, 4 -trimethoxyphenyl)-tropone, 2-methoxyestradiol Alignment models for compounds under analysis [33]... 

R147 R. S. Prosser and C. R. Sanders II, Solid State NMR Approaches to the Study of Membrane Proteins in Magnetically Aligned Model Membranes , p. 207... 

Neuwald, A. F., et al., Extracting protein alignment models from the sequence database. Nucleic Acids Res, 1997. 25(9) p. 1665-77. 

Yu, C.-N., Joachims, T., Elber, R., PiUardy, J. Support vector training of protein alignment models. In Research in Computational Molecular Biology. Lecture Notes in Computer Science, vol. 4453. Berlin Springer/Heidelberg 2007, pp. 253-67. 

We distinguish three ways to simulate the configurational confinement of network strands. In the slip-link model each strand threads its way through a number of small rings. Such an approach has also been used successfully in calculating the viscoelastic properties of polymer melts The topological contributions are caused by the orientation of the subchains between the slip-links, i.e. the slip-link model may be called an alignment model. 

Fig. 6.14. Ion beam incidence angular dependence of the liquid crystal pretilt angle (3 and the molecular tilt angle 7 of the polymer segment distribution at the film surface for polyimide (top) and amorphous carbon (bottom). As predicted by the alignment model the liquid crystal pretilt angle / follows the molecular tilt angle 7. The line is a fit to y 0) using a model that assumes finite, but different cross sections for breaking of phenyl rings oriented along or perpendicular to the ion beam direction [35].

Fig. 6.10. (A) Liquid crystals align on rubbed and ion beam irradiated polyimide surfaces along the treatment direction, but with opposite pretilt angles. (B) The respective polarization dependences possess the same overall orientation, but opposite shifts with respect to a = 0° within the plane parallel to the rubbing direction (solid squares). This is in agreement with the presented alignment model, as the derived molecular distribution factors illustrate (C).

Wu Z, Hruby VJ. Backbone alignment modeling of the structure-activity relationships of opioid ligands. J Chem Inf Model. 2011 51 1151-64. 

With respect to interpreting these results in terms of a dipole alignment model, it would appear unwise to do this, at least relative to the current studies. The actual values of the contributions of various terms are given in the text. In particular, for the case of a single H2O...formamide complex, the dipole term is not the only major contributor, and significant contributions were usually observed... 

Fig. 2.11 Alignment model for a main chain polymer for low pretilt (a) before rubbing, (b) after rubbing. Permission to print from [32], courtesy Society for Information Display.

Fig. 2.28 Alignment models of nematic LC on rubbed polyimide surface. Reproduction by permission from [33].

Fig. 2. 35 Alignment model around the spacer beads. The left side is the alignment model when there are no electric fields. The right side is that when the electric field is applied to the LC cell. When the electric field is applied to the LC cell, the disclination lines extend asymmetrically to the rubbing direction on the glass substrates because of the pretilt ai e of the LC molecules.

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