The Protein Folding Problem

Problem 3   Given a sequence of amino acids, predict the 3D structure of the protein.

Since the functionality of the protein is determined by its 3D structure, it would be very helpful to be able to predict the protein's structure, thus helping to understand its role and responsibilities in the cell. There are several approaches towards this problem. The first, called homology, uses a protein database to search for similar sequences of proteins. If such a protein is found (a protein with $25\%$ of the amino-acids in its sequence being identical to the original is usually similar enough), it is quite safe to assume that the two proteins will have the same structure. The second approach, threading, classifies known structures into families with similar foldings. Given a sequence of amino acids, we select the family to which the given sequence is most likely to fold. A third approach, de novo (from Scratch), tries to find the structure which minimizes the energy of the protein.