Molecular modeling homology

This study of such of an electron transfer chain is most timely, since the 3D structures of all the components involved are known (and related components can easily be obtained by homology molecular modeling). Proposals of structural models for the complexes formed between D. gigas AOR and flavodoxin, based on the available X-ray... 

Lewis DF, Lake BG, Bird MG. Molecular modelling of human microsomal epoxide hydrolase (EH) by homology with a fungal (Aspergillus niger) EH crystal structure of 1.8 A resolution structure-activity relationships in epoxides inhibiting EH activity. Toxicol In Vitro 2005 19 517-22. 

For Trichoderma reesei the cellulases most thoroughly investigated with respect to their structural properties are CBH I and CBH II and to a lesser extent the two en-doglucanases (EG I and EG III) 11 (Table I). For most other cellulases structural characterizations are confined to the amino add sequence as deduced from the base sequence of the respective genes and to sequence related investigations such as hydro-phobic cluster analysis 10 or computer aided molecular modelling and homology... 

Lewis, D. F. and Lake, B. G. (1999) Molecular modelling of CYP4A subfamily members based on sequence homology with CYP102. Xenobiotica 29, 763-81. 

Lewis, D. F. V., Wiseman, A., and Tarbit, M. H. (1999) Molecular modeling of lanosterol 14-alpha-demethylase (CYP51) from Saccharomyces cerevisiae via homology with CYP102, a unique bacterial cytochrome P450 isoform quantitative structure-activity relationships (QSARs) within two related series of antifungal azole derivatives../. Enz. Inhib. 14, 175-192. 

Lewis, D.F.V. et al. (2002) Molecular modelling of the human glucocorticoid receptor (hGR) ligand-binding domain (LBD) by homology with the human estrogen receptor a (hERa) LBD quantitative structure-activity... 

Figure 8-20 MolScript ribbon drawings of the OmpF porin of E. coli. (A) View of the 340-residue monomer. (B) View of the trimer looking down the threefold axis. From Wa-tanabe et al3is From atomic coordinates of Cowan et al.3i9 (C) Molecular model of the constriction zone of the PhoE porin. Locations of key residues are shown, with positions of homologous residues in OmpF given in parentheses. Extracellular loops have been omitted. Constructed from coordinates of Cowan et al.349 by Samartzidou and Del-cour.342 Courtesy of Anne Delcour.

This chapter focuses on the application of molecular modeling to calculate, manipulate, and predict protein structures and functions. Concepts of structure similarity/ overlap, homology modeling, and molecular docking, which are special concerns of protein biochemists, are considered. Approaches to protein modeling by the use of two programs (Swiss-Pdb Viewer and KineMage) and two online servers (B and CE) are described. 

Key Words G Protein-coupled receptors serotonin receptors rhodopsin sequence homology molecular models protein structure. 

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