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A normal protein can be composed of about 10000 amino-acid residues, that is something like 100000 atoms, but large proteins exist composed by more than 500000 atoms. All these atoms are not randomly distributed, but forms a complex and ordered structure, called the protein secondary and tertiary structure.

Just to make the situation more complex, several proteins sometimes join together to form protein complexes, like the heart Troponin complex.

As all biomolecules proteins react with other molecules in specific sites, called active sites for the considered reactant. Naturally different active sites exist, for different molecules with which the protein can react.

The possibility of a protein to react with a certain molecule depends not only from the presence of a suitable active site that binds with the considered molecule, but also from the protein shape, the so called steric factor. For example, if the protein shape enclosed the active site withing a sort of shell, that renders impossible to the other molecule to reach it, the reaction cannot happen even in the presence of a suitable active site.

last, but not least, reaction is possible frequently only in suitable environmental conditions like pH, reagents concentrations, presence of enzymatic catalysis and so on.

Such a complexity is very difficult to manage without the help of a computer that allows the huge number of possible situations to be managed.

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