Nearest-neighbor analysis

Wang, K., and Richards, F. (1974) An approach to nearest neighbor analysis of membrane proteins. Application to the human erythrocyte membrane of a method employing cleavable cross-linkages. J. Biol. Chem. 249, 8005-8018. 

Next, supervised-learning pattern recognition methods were applied to the data set. The 111 bonds from these 28 molecules were classified as either breakable (36) or non-breakable (75), and a stepwise discriminant analysis showed that three variables, out of the six mentioned above, were particularly significant resonance effect, R, bond polarity, Qa, and bond dissociation energy, BDE. With these three variables 97.3% of the non-breakable bonds, and 86.1% of the breakable bonds could be correctly classified. This says that chemical reactivity as given by the ease of heterolysis of a bond is well defined in the space determined by just those three parameters. The same conclusion can be drawn from the results of a K-nearest neighbor analysis with k assuming any value between one and ten, 87 to 92% of the bonds could be correctly classified. 

Nearest neighbor analysis. A technique developed by Komberg and associates before the availability of sequencing methods is the nearest neighbor sequence... 

Fia. 6. Scheme for nearest neighbor analysis of phosphodiesters formed in the ligase reaction. From Weiss et al. (66a). 

Nearest Neighbor Analysis of Nucleotides Joined in Ligase Reaction 6... 

Tomo T, Enami I, Satoh K. Orientation and nearest neighbor analysis of psbl gene product in the photosystem II reaction center complex using bifunctional cross-linkers. FEBS Lett 1993 323 15-18. 

In several mammalian genomes, between 1% and 7% of C residues in DNA are methylated, and more than 90% of these have a G following them. Nearest-neighbor analysis done with a computer also reveals that the dinucleotide of highest frequency in the mammalian genomes is TG. An explanation of this phenomenon is that thymine residues can be the product of the spontaneous deamination of methylcytosine (Fig. 7-2). Corruption of the code by this means may not be detected by DNA repair mechanisms (Chap. 8), so such a change in a somatic cell will persist into the next generation derived from it. 

---