Assessment of some problems associated with prediction of the three-dimensional structure of a protein from its amino-acid sequence

Abstract

It is shown that most present empirical prediction algorithms provide information about the conformational states of individual residues, but give little information about the three-dimensional structure of a protein. It is necessary to predict the conformational state of every residue before the resulting structure can serve as a starting conformation to compute the native structure. It is also shown that even a perfect five-state algorithm (which does not include long-range interactions from disulifide loop closing or solvation) will not lead to a globular structure resembling the native one. However, starting from the results of a perfect prediction algorithm, it appears that conformational energy minimization (with long-range interactions included) can lead to a structure having the general features of the native protein.