Structure-function drug design

In general the relevance of predictions of structure-function relationships based on molecular modeling and structural bioinformatics are threefold. First they can be used to answer the question of which partners (proteins) could interact. Second, predictions generate new hypotheses about binding site, about molecular mechanisms of activation and interaction between two partners, and can lead to new ideas for pharmacological intervention. The third aim is to use the predictions for structure-based drug design. 

The conditio sine qua non for structure-based drug design is the identification and functional annotation of the relevant binding site(s) in a target protein. A number of methods, closely related to the characteristics of binding sites and the restraints imposed on the formation of functional structural units, are discussed in Section 4.2. The most commonly used methods can be classified into geometry-based methods for cavity detection, methods for identifying specific patterns, and evolutionary methods. 

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