Prediction by restraint driven folding Evolutionary based approaches

Prediction by restraint driven folding Evolutionary based approaches. 

Approaches to structure prediction using different flavors of secondary structure constraints have been recently reported. This renewed interest in the use of secondary structure information as a way of reducing conformational space when building molecular models is the result of the recent improvement in accuracy of secondary structure prediction methods due to the introduction of evolutionary information. 

Evolutionary approaches based on correlated residue mutations 

1996 review So far, none of the methods appears to find a path between the Scylla of missing too many true contacts and the Charybdis of predicting to many false contacts . An analysis of the methods available indicated that two effects were mainly responsible for the poor performance of the contact map prediction the clustering of sequences in subfamilies (the subfamily effect ) and the presence of indirect, or multiple, correlations among different positions in the alignment. 

In MONSSTER, a secondary structure bias is incorporated using a penalty function for those residues having a predicted secondary structural type, energetic biases for the various allowed conformational states are assigned 

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