Methods for determining correlated residues in a protein or other biopolymer using molecular dynamics

The invention provides methods and systems of determining biopolymer profiles and correlations between structural units ( residues) of a biopolymer based on sampling of the conformational space available to the molecule. The correlations between these structural units can further be used to find networks within a biopolymer such as the coupled residue networks in a protein. The invention also provides for designing and engineering biopolymers including polypeptides, nucleic acids and carbohydrates using the information derived from the conformation clustering and subsequent methods described herein.