A lattice model for protein structure prediction at low resolution (protein folding/tertiary structure/conformational search)
2016
The prediction of the folded structure of a protein from its sequence has proven to be a very difficult computational problem. We have developed an exceptionally simple representation of a polypeptide chain, with which we can enumerate all possible backbone conformations of small proteins. A protein is represented by a self-avoiding path of connected vertices on a tetrahedral lattice, with several amino acid residues assigned to each lattice vertex. For five small structurally dissimilar proteins, we find that we can separate native-like structures from the vast majority of non-native folds by using only simple structural and energetic criteria. This method demonstrates significant generality and predictive power without requiring foreknowledge of any native struc- tural details. The three-dimensional structures of protein molecules are thought to be largely if not completely determined by their amino acid sequences (1, 2). However, the prediction of
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