Tertiary protein structure predictions, derivation from

Ortiz, A. R., A. Kolinski, and J. Skolnick, Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. Proteins, 1998. 30(3) p. 287-94. 

Present practical methods to derive a three-dimensional model of a protein from Its sequence, however, use a tertiary template such as crystal structures of other proteins closely related by sequence to the protein to be modeled Q, 2 ). When the crystallographic data are not available for related proteins, predictions have so far been too low In reliability to evaluate the energy of Interactions between the protein and a drug molecule, and to optimize the chemical structure of a drug to fit into the active site In a satisfactory way. Even In the prediction of secondary structures, the match between the observed and the estimated Is as low as 50-60% at most O, ). The low success score of structure prediction limits the availability of sequence Information for drug design. 

What can be done by predictive methods if the sequence search fails to reveal any homology with a protein of known tertiary structure Is it possible to model a tertiary structure from the amino acid sequence alone There are no methods available today to do this and obtain a model detailed enough to be of any use, for example, in drug design and protein engineering. This is, however, a very active area of research and quite promising results are being obtained in some cases it is possible to predict correctly the type of protein, a, p, or a/p, and even to derive approximations to the correct fold. 

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