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 programPro—Anal for analysis of the structure-activity relationshipin a family of evolutionarily related (and/or artificially mutated)proteins/peptides. The program uses aligned amino acid sequenceswith data of their activity (pK, K_m, ED₅₀ or any other) andsearches for correlations between data on activity and variousphysico-chemical characteristics of different regions in primarystructures. In automatic mode, the program generates and verifieshypotheses on the disposition of a sequential modulating regionin a protein, and key characteristics of the region. In manualmode, users can generate and analyze their own hypotheses. Theprogram is implemented on IBM PC or compatible computers. Itis designed to be easily handled by the occasional computeruser and yet it is powerful enough for experienced professionals.Pro—Anal operation is demonstrated on the example of findingmodulating centers in a family of disintegrins—proteinsfrom snake venoms which inhibit fibrinogen interaction withplatelet receptors. In another example it is shown that theimmunogenicity of peptides is connected with their positivecharge.