Protein Residues, Homology Modeling

The 3D models are generally evaluated by relying on geometrical preferences of the amino acid residues or atoms that are derived from known protein structures. Essential for interpreting 3D protein models is the estimation of their accuracy, both the overall accuracy and the accuracy in the individual regions of a model. The errors in models arise from two main sources, the failure of the conformational search to find the optimal conformation and the failure of the scoring function to identify the optimal conformation. 

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For many protein drug targets crystal or solution structures are not available. In such cases homology models (130,131)and pseudoreceptor models (132) are often used. However, unless there is a very high conservation of receptor site residues the use of homology models for virtual screening is much riskier than using solved structures. On the other hand, the PDB contains a wealth of protein... 

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