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Assessment and Refinement of the Structure

Assessment and Refinement of the Structure: The structural features of the models developed using the homology modeling should reasonably match the proteins three dimensional structure. That is, researchers have analyzed three-dimensional structures of proteins from which basic principles of protein structure and folding have been developed. There are many programs available to help in the analysis of the correctness of a homology model. The criteria for analysis of correctness can include:

• major chain conformations in acceptable areas of the Ramachandran map
• planar peptide bonds
• side chain conformations which correspond to such in the rotamer library
• hydrogen-bonding of polar atoms when they are buried
• appropriate environments for hydrophobic and hydrophilic residues
• no bad atom-atom contacts
• no wholes inside the structure.

There are many programs that check the analysis of a structure. Example is PROCHECK. PROCHECK is based on an analysis of (phi, psi) angles, peptide bond planarity, bond lengruths, bond angles, hydrogen-bond geometry, and side-chain conformations of identified protein structures as a function of atomic resolution.

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