Tertiary restraints

Prediction Using Known Secondary Structure and Correct Tertiary Restraints... 

The rationale is that in this way it is possible to restrict the predictions to rigid elements of the core, for which the assumption of closeness in space as reflected in the covariance of their mutational behavior is, in principle, more valid. Then, inverse folding [226] is used to select compatible fragments in contact, thereby enriching the number and identity of predicted side-chain contacts. Parenthetically, we note that for topological elements that are known to touch, this procedure produces contacts of which 67% are correct within +1 residue. This is of comparable accuracy to the situation where the contacts are predicted. Of course, they do not employ any information about the native structure in the prediction protocol. The final outcome of the prediction protocol is a set of noisy secondary and tertiary restraints. 

Kihara, D., Lu, H., Kolinski, A., Skolnick, J. TOUCHSTONE An ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc. Natl. Acad. Sci. USA 2001, 98, 10125-30. 

Secondary and tertiary restraints in assembly of protein structures... 

Models with exact secondary structure but no tertiary restraints... 

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