title: 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.
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D005069:Evaluation Studies as Topic; D008433:Mathematics; D008722:Methods; D008958:Models, Molecular; D008968:Molecular Conformation; D011487:Protein Conformation; D014961:X-Ray Diffraction
chemical_list: D000596:Amino Acids