ABSTRACT
The resonant recognition model (RRM) belongs essentially to the field of protein and DNA sequence analysis. Scientific efforts in this field can be classified into two groups of approaches: (1) Mathematical analysis of amino acid or nucleotide arrangement with the aim to search for information on biological function, and (2) analysis of physical processes inside the macromolecule which could be relevant to its biological function. The most commonly used method from the first group is homology searching. The main idea behind this method is that sequences with the same biological functions do have a part of the sequence in common and that this part carries the main information about the function. This method is very useful in the case of conserved sequences (Le., histones, hemoglobins, insulins, etc.) or of some DNA regulatory sequences, where the existence of a specific core sequence of five to seven nucleotides was established. For promoters this is the TATA boxl and for enhancers this is the GTGC-GT box.2 But there are many examples of sequences that display the same biological activity but do not have a significant degree of homology, and there are also examples with a significant degree of homology between functionally unrelated sequences. The belief is that homology denotes the same ancestry molecule but not a similar function. 3 There are also other, mostly statistical methods, which are not in common use due to the limits of their application. Most of them are presented in the University of Wisconsin software package. 4
The hydropathy tnethod of R. Doolittle3 is a method of sequence analysis that belongs essentially to the first group of methods but has elements of a physical approach as well. The main idea behind this approach is to represent a protein sequence as a numerical sequence by representing each amino acid with a corresponding hydropathy value. After smoothing this curve it is possible to see the distribution ofhydropathy along the sequence. This is important for estimation of the active part of the protein.
