Protein Structure Comparison

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

Three-Dimensional Considerations Discrimination of common protein folds application of protein structure to sequence/structure comparisons, 266, 575 three-dimensional profiles for measuring comparability of amino acid sequence with three-dimensional structure, 266, 598 SSAP sequential structure alignment program for protein structure comparison, 266, 617 understanding protein structure using scop for fold interpretation, 266,... 

The publication of Mitchell et al. (1990) [52] led to interest in other groups in the use of graph theoretical methods for protein structure comparison. Notable... 

Chambers JL, Stroud RM (1979) The accuracy of refined protein structures comparison of two independently refined models of bovine trypsin. Acta Cryst B35 1861-1874... 

Holm, L., and Sander, C. (1995). Dali A network tool for protein structure comparison. Trends Biochem. Sci. 20, 478—480. 

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]... 

Orengo, C. A. and W. R. Taylor, SSAP sequential structure alignment program for protein structure comparison. Methods Enzymol, 1996. 266 p. 617-35. 

May, A. C. and M. S. Johnson, Improved genetic algorithm-based protein structure comparisons pairwise and multiple superpositions. Protein Eng, 1995. 8(9) p. 873-82. 

Taylor W. R., Protein structure comparison using iterated double dynamic programming. Protein Sci, 1999. 8(3) p. 654-65. 

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

Another important application of clustering in life sciences is molecular, particularly protein, structures comparison. Most of the comparative analysis involves the direct alignment and superimposition of stmctures in a three-dimensional space (Xiong, 2006). According to (Xiong, 2006). The stmcture comparison is one of the fundamental techniques in protein stmcture analysis for three reasons (a) it can detect remote protein homologs, since stmctural comparison can reveal distant evolutionary relationships between proteins (b) it is a prerequisite for protein stmctural classification and (c) comparison of theoretically known stmctures with experimentally predicted ones is a critical procedure in the evaluation of protein stmcture prediction methods. 

A. C. W. May and M. S. Johnson, Protein Eng, 7, 475 (1994). Protein Structure Comparisons Using a Combination of a Genetic Algorithm, Dynamic Programming and Least-Squares Minimization. 

The most difficult application of protein structure comparison comes in classifying known protein structures into different clusters corresponding to fold families. The role of such classifications is to organize structure databases such as the PDB, in hopes of detecting similarities at the structure level that... 

---