Protein structure homology modeling

Arnold K, Bordoli L, Kopp J et al (2006) The SWISS-MODEL workspace a web-based environment for protein structure homology modelling. Bioinformatics 22 195-201... 

Repository of Annotated Three-Dimensional Protein Structure Homology Models. The SWISS-MODEL repository http //swissmodel.expasy.org/repository/. 

SWISS-MODEL. (2011). A fully automated protein structure homology-modeling server, http // swissmodel.expasy.org/. Retrieved 10 Mar 2011. 

L. Bordoli, F. Kiefer, K. Arnold, P. Benkert, J. Battey, and T. Schwede, Nat. Protoc., 4, 1-13 (2009). Protein Structure Homology Modeling using SWISS-MODEL Workspace. 

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]. 

More recently, Afzelius and co-workers used GRID/CPCA for a comparative analysis of protein structures of GYP2C9 and CYP2C5 from different sources crystal structures, homology models, and snapshots from molecular dynamics simulations [16]. The evaluation of molecular dynamics simulations by means of GRID/GPGA is an especially interesting new aspect in their publication. 

P Koehl, M Delame. A self consistent mean field approach to simultaneous gap closure and side-chain positioning m protein homology modelling. Nature Struct Biol 2 163-170, 1995. R Samudrala, J Moult. A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol 279 287-302, 1998. 

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