Algorithm and computer program Pro—Anal for analysis of relationship between structure and activity in a family of proteins or peptides

In this paper we introduce a computer algorithm and program Pro—Anal for analysis of the structure-activity relationship in a family of evolutionarily related (and/or artificially mutated) proteins/peptides. The program uses aligned amino acid sequences with data of their activity (pK, K_m, ED₅₀ or any other) and searches for correlations between data on activity and various physico-chemical characteristics of different regions in primary structures. In automatic mode, the program generates and verifies hypotheses on the disposition of a sequential modulating region in a protein, and key characteristics of the region. In manual mode, users can generate and analyze their own hypotheses. The program is implemented on IBM PC or compatible computers. It is designed to be easily handled by the occasional computer user and yet it is powerful enough for experienced professionals. Pro—Anal operation is demonstrated on the example of finding modulating centers in a family of disintegrins—proteins from snake venoms which inhibit fibrinogen interaction with platelet receptors. In another example it is shown that the immunogenicity of peptides is connected with their positive charge.