Alignment structure

Holm L and C Sander 1994. The FSSP Database of Structurally Aligned Protein Fold Families. Ni Acids Research 22 3600-3609. 

Holm L and C Sander 1999. Protein Folds and Families Sequence and Structure Alignments. Ni Acids Research 27 244-247. 

Orengp C A, N P Brown and W R Taylor 1992. Fast Structure Alignment for Protein Datal Searching. Proteins Structure, Function and Genetics 14 139-167. 

Orengo C A and W R Taylor 1990. A Rapid Method of Protein Structure Alignment. ]oumal ofTheon Biolo y 147 517-551. 

C and T Lengauer 2000. Computational Methods for the Structural Alignment of Molecules. nal of Computer-Aided Molecular Design 14 215-232. 

L Holm, C Sander. Protein folds and families Sequence and structure alignments. Nucleic Acids Res 27 244-247, 1999. 

KK Koretke, Z Luthey-Schulten, PG Wolynes. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Protein Sci 5 1043-1059, 1996. 

McDonnell, A. V., Menke, M., Palmer, N., King, J., Cowen, L., and Berger, B. (2006). Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins. Proteins 63, 976-985. 

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).

Gotoh, O. (1996). Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. /. Mol. Biol. 264, 823-838. 

Structural alignments (ligand-based virtual screening) on the basis of a known active compound, molecules that show a good superimposition in shape and physicochemical features are searched for. 

For most of the classes, recent review articles can easily be found Molecular docking [6-10], Structural alignments [11, 12], Molecular similarity [13-15], Pharmacophore mapping [16-18]. 

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