Sequence-structure compatibility

Lin, K., May, A.C.W., Taylor, W.R. Threading using neural network (TUNE) The measure of protein sequence-structure compatibility. Bioinformatics 2002,18,1350-7. 

Y. Matsuo and K. Nishikawa, Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci. 3, 2055-2063 (1994). 

The Objective Function Measures of Sequence -Structure Compatibility... 

Diblock copolymers, as illustrated in Fig. 5.8 c), comprise homopolymer sequences of the two monomers linked together. The homopolymer blocks may be either compatible or incompatible, depending on their chemical structure. If the sequences are compatible, they will mix to form a material with characteristics similar to those of a blend of the two homopolymers. On the other hand, if the blocks are incompatible, they will tend to segregate from one another to form distinct phases. Each phase will display properties characteristic of the homopolymer, modified by the constraints placed on them by having one end attached... 

IgE antigens combined with in vitro tests of cross-reactions of IgE and sequenced antigens, as it has been found that the basic condition for positive cross-reactivity is the high structural compatibility (homology) of reagents. Compared to B-cells, T-cell cross-reactivity is far more difficult to assess because the mechanism of T-cell effects is more diverse and involves both the phase of immunological response and the effect phase of the allergic reaction. 

Figure 2. Mapping active variants and structural hypotheses. The relation, c 5 X for an hypothetical example. The sequence variants are identified by 5 for i = 1,2,3,4,5 and the structural hypotheses by for j = 1,2,3,4. The lines indicate which sequences are compatible with which structural hypotheses as determined by the generation of consistent models by the MC-SYM program. Here were found consistent with the three-dimensional models of ff,.

However, given the biological supposition that the active conformation should be found among the structures common to all sequences, the belief coefficients were assigned according to how many sequences are compatible with the hypothesis, that is, for 51,5, the belief coefficient of sequences 5i, and S5,... 

Figure 7 Schematic of a genetic algorithm for sequence design. Hydrophobic residues are symbolized in black. Sequences are evaluated according to a function measuring their compatibility with the target structure. Compatible. sequences - ones that form hydrophobic clusters in our example - are preferentially replicated to form a new pool, which is then subjected to variation. Crossing over of sequences conserves locally optimal. solutions mutations allow further optimization. The procedure is iterated to convergence...

If one expects the database potentials to identify compatible sequence-structure combinations from a large number of alternatives, it is important to find out if they can provide reasonable estimates of the stability changes produced by substitutions in individual sequence positions. One could indeed envisage that performing many such substitutions at once is equivalent to mounting a new sequence onto the same protein fold. 

Upper-case lettering refers to cations, lower-case lettering to anions, and the notation used is that for close-packed sequences. The compatability of the two structures in these directions is obvious. 

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