Alignment sequence-structure

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. 

Catherinot, V. and Labesse, G. (2004) VITO tool for refinement of protein sequence-structure alignments. Bioinformatics, 20 3694-3696. 

For fold recognition, the amino acid substitution matrix can be replaced by a 3D-ID substitution matrix (scoring table) computed from a database of known structures and sets of sequence-structure alignments (Bowie et al., 1991). Recently, the matrix has been further extended to include predicted secondary structure of the sequence using a H3P2 matrix (Rice Eisenberg, 1997). The 3D-ID substitution matrix allows one to match the amino acid residues (and/or their secondary structure prediction) with structural (environmental) classes. 

Pair potentials vs contact capacity potentials a) a pair potential attributes an energetic contribution to each pair of amino acids a, and aj that are mapped by a sequence-structure alignment onto locations of the amino acids b and b/ of the protein template structure. The contribution depends on the types of residues a, and aj as well as on geometric features of their locations b/, and b/, such as their distance in space or in sequence. Often, only certain pairs of amino acid residues are scored, such as those that are contacting or close in space. The total energy is computed as the sum of all pair contributions, b) a contact capacity potential rates the energetic contribution of an amino acid a, from the protein target... 

The involved alignment optimization problem, i.e. the problem of finding a sequence-structure alignment with minimum pair interaction score is NP-complete [38],... 

The following section discusses methods for computing sequence-structure alignments for both types of scoring functions. 

The algorithmic viewpoint on sequence-structure alignment and threading... 

Bryant Gibbs Threading Gibbs sampling for sequence-structure alignment with contact potentials... 

Zimmer, R. and R. Thiele, Fast Fold Recognition and accurate sequence-structure alignment, in GCB96. 1997 Springer Verlag. 

Sometimes motifs are also used interchangeably with patterns to describe recurring, conserved sequences of functional significance derived from sequence/structure alignment studies. In this usage, motifs (patterns) are commonly associated with specific functions of homologous proteins (Table 5.6). 

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