Model building rotamer library

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

The second approach to dealing with poor data is the use of standard conformation libraries [3], It is clear that the use of perfect coordinates in such libraries to help building the model is to be preferred over coordinates with errors. However, there is one danger in the use of standard libraries circularity. Take, for example, side chain conformation libraries [3,18,19]. Residues positioned in a structure purely based on such a database will not easily be flagged as incorrect by rotamer... 

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