Classification of Complex Molecules

Algorithms for classification and taxonomy based on criteria, e.g., information entropy and its production are proposed. In molecular classification, the feasibility of replacing a given molecule (e.g, anaesthetic) by similar ones in the composition of a complex drug is studied. Some local anaesthetics currently in use are classified using characteristic chemical properties of different portions of their molecules. In taxonomy, the detailed comparison of the sequences (primary structures) of biomolecules, proteins or nucleic acids, allows the reconstruction of a molecular phylogenetic tree for some species, e.g. the 1918 influenza virus. The method is applied to the classifications of: (1) indazolols (action against Trichomonas vaginalis), (2) fullerenes, fullerite and single-wall carbon nanotubes, (3) living and heat-inactivated lactic acid bacteria against cytokines, (4) phylogenesis of avian birds and of the 1918 influenza virus, (5) local anaesthetics (analogues of procaine), (6) transdermal-delivery percutaneous enhancers, (7) quantitative structure-activity relationship modelling of anti-human immunodeficiency virus type 1 (HIV-1) compounds and (8) HIV-1 inhibitors. If, in the calculation of entropy associated with the phylogenetic tree, a species is systematically omitted, the difference between the entropy with and without this species can be considered as a measure of the species entropy. Such contributions may be studied with the equipartition conjecture. Obviously, it is not within the scope of our simulation method to replace biological tests of drugs or field data in palaeontology, but such simulation methods can be useful to assert priorities in detailed experimental research. Available experimental and field data should be examined by different classification algorithms to reveal possible features of real biological significance.