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12 Consensus Drug Design Using IT Microcosm
12.2.1 Concepts
The IT Microcosm paradigm goes as follows: The biological activity of a chemical
compound is determined by the complex effect of this compound as a whole on all
of the components of a biological system by multiple characteristics of its structures
[96, 105, 99, 110]. By extension, we consider the properties of a compound instead
of its biological activity and a high-complexity dynamic chemical system instead
of a biological system.
The semantic content of the IT Microcosm paradigm is a complex methodology for the computer prediction of the properties of a chemical compound. This
methodology is founded on uniting the following for calculations: various ways of
representing the chemical structure that differ in their physicochemical meaning,
various levels of representing the chemical structure that differ in their complexity,
redundant representations of the chemical structure that expand its parameters, classification methods that vary in their mathematical formalism, and decision circuits
that are conceptual in the results they yield [105, 122]. Because it synthesizes all
of the above mentioned components, the complex methodology produces contextindependent decision rules (i.e., rules that do not depend on the composition of
the training set, the ways of representing compound structures, or the methods of
recognizing regularities) and predictive estimates of biological activity founded
on these rules. The IT Microcosm paradigm comprises several basic theoretical
concepts: high-complexity dynamic chemical systems, a generalized pattern of a
class of compounds with desired property, a multidescriptor hierarchic multilevel
representation of the structure of a chemical compound, mega-dimensional spaces,
complementarity of the decision rules for the computer prediction of chemical compound properties, and strategies for the computer prediction of chemical compound
properties.
A high-complexity dynamic chemical system (hereafter referred to as a complex
chemical system) [95] is defined as an entire system containing a large number of
individual chemical compounds contained in a space with a limited volume; these
compounds interact with one another and the external environment and are separated from the external environment and one another by one or more semipermeable
surfaces.
The activity of a chemical compound can be defined as the ability of this compound to cause a change in the value of one or more external parameters in a complex chemical system by a system interaction. The methods that were developed
to predicting the activity of a compound in a certain complex chemical system can
be applied to other complex chemical systems with minor adjustments. A complex
chemical system recognizes a chemical compound through the sum of its characteristics, where each characteristic in isolation is of no great consequence. An active
compound interacting with a complex chemical system is regarded as an object with
a large number of degrees of freedom. An adequate description of such an object
is only possible using a huge number (ideally, an infinite number) of parameters
that differ in their physical and chemical meanings. The complex chemical system
responds to components with varying degrees of complexity and at different stages.
12 Consensus Drug Design Using IT Microcosm
12.2.1 Concepts
The IT Microcosm paradigm goes as follows: The biological activity of a chemical
compound is determined by the complex effect of this compound as a whole on all
of the components of a biological system by multiple characteristics of its structures
[96, 105, 99, 110]. By extension, we consider the properties of a compound instead
of its biological activity and a high-complexity dynamic chemical system instead
of a biological system.
The semantic content of the IT Microcosm paradigm is a complex methodology for the computer prediction of the properties of a chemical compound. This
methodology is founded on uniting the following for calculations: various ways of
representing the chemical structure that differ in their physicochemical meaning,
various levels of representing the chemical structure that differ in their complexity,
redundant representations of the chemical structure that expand its parameters, classification methods that vary in their mathematical formalism, and decision circuits
that are conceptual in the results they yield [105, 122]. Because it synthesizes all
of the above mentioned components, the complex methodology produces contextindependent decision rules (i.e., rules that do not depend on the composition of
the training set, the ways of representing compound structures, or the methods of
recognizing regularities) and predictive estimates of biological activity founded
on these rules. The IT Microcosm paradigm comprises several basic theoretical
concepts: high-complexity dynamic chemical systems, a generalized pattern of a
class of compounds with desired property, a multidescriptor hierarchic multilevel
representation of the structure of a chemical compound, mega-dimensional spaces,
complementarity of the decision rules for the computer prediction of chemical compound properties, and strategies for the computer prediction of chemical compound
properties.
A high-complexity dynamic chemical system (hereafter referred to as a complex
chemical system) [95] is defined as an entire system containing a large number of
individual chemical compounds contained in a space with a limited volume; these
compounds interact with one another and the external environment and are separated from the external environment and one another by one or more semipermeable
surfaces.
The activity of a chemical compound can be defined as the ability of this compound to cause a change in the value of one or more external parameters in a complex chemical system by a system interaction. The methods that were developed
to predicting the activity of a compound in a certain complex chemical system can
be applied to other complex chemical systems with minor adjustments. A complex
chemical system recognizes a chemical compound through the sum of its characteristics, where each characteristic in isolation is of no great consequence. An active
compound interacting with a complex chemical system is regarded as an object with
a large number of degrees of freedom. An adequate description of such an object
is only possible using a huge number (ideally, an infinite number) of parameters
that differ in their physical and chemical meanings. The complex chemical system
responds to components with varying degrees of complexity and at different stages.