Protein Structure Analysis ProSa

The energies of the protein structure are converted in ProSa into a Z-score (Eq. [6] ). The best protein model has the lowest Z-score when compared with all other protein structures. The Z-score is composed of three components the knowledge-based energy of sequence S in a specific conformation C (Es c)j the average energy of the sequence in all conformations of a database (Es), and the standard deviation ess) associated with the average energy of the 

Comparing the Z-score of the database with that of a modeled target protein provides a method of determining the viability of the target model. The energy of the modeled target protein is E, x where X is the observed structure of the 

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ProSa potentials derive from a knowledge base of globular, soluble protein structures. If they are applied to the analysis of proteins with different characteristics (such as membrane proteins), the results may lead you astray. 

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