Homology Conformation search

CA Schiffer, JW Caldwell, PA Kollman, RM Stroud. Prediction of homologous protein structures based on conformational searches and energetics. Pi otems 8 30-43, 1990. 

C Wilson, LM Gregoret, DA Agard. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol 229 996-1006, 1993. 

G-Protein-coupled receptors do not lend themselves to analysis by either NMR or x-ray crystallography due to their structural dependence on an intact cell membrane. In our laboratories we pursued this valuable structural information by utilizing a combination of structural homology modeling, molecular dynamics, systematic conformational searching methods, and mutagenesis experiments. The combination of these techniques led to a proposed model of bradykinin bound to the agonist site on its receptor [41]. 

Abagyan, R., Batalov, S., Cardozo, T., Totrov, M., Webber, J., and Zhou, Y. (1997) Homology modeling with internal coordinate mechanics deformation zone mapping and improvements of models via conformational search. Proteins Suppl 1, 29-37. 

Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN application in predicting the three-dimensional structure of murine homeodomain Msx-1. 

It is interesting to note that AIMB could be considered to be the parent of the entire field of protein homology modeling, since both of these methods utilize analogy to known structures as the basis of the modeling method. Since hundreds of papers have been written on this one specific type of conformational searching, this topic is handled as a separate article in this encyclopedia. 

Here we restrict consideration to two well-defined conformational search problems that routinely occur in the modeling of protein structures from the known structure of a homolog " (see Supetfamily Analysis Understanding Protein Function from Structure and Sequence). 

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