Comparative modelling of proteins

N Srimvasan, TL Blundell. An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure. Protein Eng 6 501-512, 1993. 

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. 

C. Hutchins, and J. Greer, Comparative modeling of proteins in the design of novel renin... 

Pons J-F, Fabesse G (2009) TOME-2 a new pipeline for comparative modeling of protein-ligand complexes. Nucleic Acids Res 37 W485-W491... 

Greer, J., Hutchins, C., Bolis, G., Fung, A., and Sham, H. Comparative modeling of proteins in the design of novel cyclic renin inhibitors. In Proteins, Renugoplakrishnan, V. (Ed.). ESCOM Leiden, Netherlands 283-289 (1991)... 

R. Samudrala, J. Moult. A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol. 1998, 279, 287-302. 

Srmivasan N, K Gurprasad and T L Blundell 1996, Comparative Modelling of Proteins. In Sternberg M E (Editor) Protein Structure Prediction - A Practical Approach. Oxford, IRL Press, pp 111-140. 

Contreras-Moreira, B., Branger, P.A., Collado-Vides, J. TFmodeUer Comparative modelling of protein-DNA complexes. Bioinformatics 2007, 23,1694-6. 

Fan, H., Irwin, J.J.,Webb, B.M., Klebe, G., Shoichet, B.K., and Sali, A. (2009) Molecular docking screens using comparative models of proteins. Journal of Chemical Information and Modeling, 49, 2512-2527. 

C. Hutchins and J. Greer, Crit. Rev. Biochem. Mol. Biol., 26, 77 (1991). Comparative Modeling of Proteins in the Design of Novel Renin Inhibitors. 

Performance of an Automated Procedure for Comparative Modeling of Protein Tertiary Structure. 

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

CM Topham, N Snmvasan, CJ Thorpe, IP Ovenngton, NA Kalsheker. Comparative modelling of major house dust mite allergen der p I Structure validation using an extended environmental ammo acid propensity table. Protein Eng 7 869-894, 1994. 

Let us turn our attention back again to the scheme illustrating various versions of the joint application of fluorescence parameters (Figure 2.1) and consider the possibilities for constructing more general and more definite models of protein dynamics. These models can be suggested and confirmed or rejected by comparing predicted behavior with the results of spectroscopic experiments of different kinds. 

Combet C, Jambon M, Deleage G, Geourjon C. 2002. Geno3D automatic comparative molecular modelling of protein. Bioinformatics 18 213-214. 

Greer J. Comparative modeling of homologous proteins. Methods Enzymol 202 1991 239-252. 

Kirton SB, Kemp CA, Tomkinson NP, et al. Impact of incorporating the 2C5 crystal structure into comparative models of cytochrome P450 2D6. Proteins 2002 49 216-231. 

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. 

Kirchmair, J., Laggner, C., Wolber, G., Langer, T. Comparative analysis of protein-bound ligand conformations with respect to catalyst s conformational space subsampling algorithms. J. Chem. Inform. Model. 2005, 45, 422-430. 

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