Protein Folding

From Biomatics.org

"Biological protein-protein interactions differ from the more general class of physical interactions; in a biological interaction, both proteins must be in their proper states (e.g. covalently modified state, conformational state, cellular location state, etc.). Also in every biological interaction, one or both interacting molecules undergo a transition to a new state. This regulation of protein states through protein-protein interactions underlies many dynamic biological processes inside cells. 
Therefore, understanding biological interactions requires information on protein states. ^" 

The Basic construction of the model protein is shown where C-alpha atoms are numbered as 1, 2, 3, etc., whereas the side residues are shown by 1', 2', 3' etc. Note the varying size of the  side residues. 

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Finite state model

The process of the folding of a protein can be described in terms of Finite State Machine(FSM) theory, one of the mathematical underpinnings of Computer Science. 

Smart molecules 
The Amino Acid Code
The Histone Code

Chaperone proteins

Chaperone proteins within the endoplasmic reticulum play an essential role in facilitating the folding of newly synthesized proteins and in recognizing and segregating misfolded proteins, thereby preventing their transit to the Golgi.

Protein Folding at Stanford
Protein Motors
Interactome.org