Featureless pattern recognition in an imaginary hilbert space and its application to protein fold classification

Abstract

The featureless pattern recognition methodology based on measuring some numerical characteristics of similarity between pairs of entities is applied to the problem of protein fold classification. In computational biology, a commonly adopted way of measuring the likelihood that two proteins have the same evolutionary origin is calculating the so-called alignment score between two amino acid sequences that shows properties of inner product rather than those of a similarity measure. Therefore, in solving the problem of determining the membership of a protein given by its amino acid sequence (primary structure) in one of preset fold classes (spatial structure), we treat the set of all feasible amino acid sequences as a subset of isolated points in an imaginary space in which the linear operations and inner product are defined in an arbitrary unknown manner, but without any conjecture on the dimension, i.e. as a Hilbert space. © Springer-Verlag Berlin Heidelberg 2001.