Scoring Structural Alignments

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. 

Panchenko, A. R. and Bryant, S. H. (2002) A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci. 11, 361-370. 

Evaluation of Structural Alignment Method Scoring by Geometric Match Measures. 

First hit (according to the Z-score value) of the structural alignment of the predicted conformation against the set of DALI representative folds of the protein data base. Bracketed names correspond to second hits. 

Z-score of the structural alignment of the predicted and experimental structures, as defined in the DALI method. 

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