Structure comparison and alignment

Structure Comparison and Alignment at CE (Combinatorial Extension) Server... 

Shindyalov, I. N., Bourne, P. E. A database and tools for 3-D protein structure comparison and alignment using the combinatorial extension (CE) algorithm. Nucl. Acids Res. 2001,29, 228-229. 

Database of 3-D Protein Structure 3-D Protein Structure Comparison and Alignment http //cl.sdsc.edu/ ce.html [297]... 

Hohn L and C Sander 1993. Protein Structure Comparison by Alignment of Distance Matrices. Joun Molecular Biology 233 123-138. 

Structure superposition and alignment Computing activities and properties of molecules often involves comparisons across a homologous series. Such techniques require superposition or alignment of structures. 

Dali structure comparison and FSSP Protein classification via structural alignment, Dali http //www2.ebi.ac.uk/dali/ [102, 293,... 

Holm, L., and C. Sander. 1993. Protein structure comparison by alignment of distance matrices. J Mol Biol 233 123-38. 

Altschul S F 1996. Sequence Comparison and Alignment. In Sternberg M E (Editor) Protein Structure Prediction - A Practical Approach Oxford, IRL Press, pp. 137-167. 

Table 10.2 Structural comparison of a-carbons and backbone atoms of CYP2B4 from different crystal structures aligned by heme group (rmsd values are given in A).

The location of the copper with respect to the Greek key fold is interesting when compared to that of the cupredoxins. While the copper in the cupredoxins lies in the interior of the /8 barrel bound by three interior-facing residues of the carboxy-terminal loop in the )8 barrel, and by a histidine in an adjacent strand, the copper in SOD lies on the outside of its jS barrel, bound by one residue from the carhoxy-terminal loop and three from the adjacent strand (cf. Figs. 2c-5c with Fig. 8c.) A structural comparison of plastocyanin and SOD, coupled with sequence alignment of plastocyanin and ceruloplasmin (Ryden, 1988), showed that three of the SOD ligands correspond to putative copper ligands in ceruloplasmin. Why this is so will become more evident after the description of the ascorbate oxidase structure and its relationship to ceruloplasmin. 

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