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... zero is unlikely to occur by chance. Other balanced scores have been proposed by Cline et al. (2002) and Yona and Levitt (2002). 9The developer’s score and the modeler’s score were first defined by (=-=Sauder et al., 2000-=-) in a slightly different way using the structure-based alignments as gold standard. In their definition, min(Lq,Lp) is replaced by the number of aligned residue pairs in the structural alignment and ...

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...e blocks), and the modeler (fM) score, defined as the number of correctly aligned residue pairs found in the test alignment divided by the total number of aligned residue pairs in the test alignment (=-=Sauder et al. 2000-=-). For each type of scoring metric used, we averaged the scores per multiple alignment (or average score per subset in the case of SABmark) over all multiple alignment tests in the database. Compariso...

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...tely, in addition to the evaluation of the ability of different methods to recognize the correct fold, some studies have also focused on the quality of the generated alignment (Domingues et al. 2000; =-=Sauder et al. 2000-=-; Bujnicki et al. 2001a; Elofsson 2001). An important conclusion from these studies is that for different targets the best predictions are often made by different methods. It is even quite common, for...

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...gs (Park et al. 1997; Muller et al. 1999; Kelley et al. 2000; Rychlewski et al. 2000; Yona and Levitt 2000; Panchenko 2003; Sadreyev and Grishin 2003) and alignment accuracy (Jaroszewski et al. 2000; =-=Sauder et al. 2000-=-; Blake and Cohen 2001; Panchenko 2003; Sadreyev and Grishin 2003), as well as optimized the alignment accuracy for protein structure prediction (Jaroszewski et al. 2000; John and Sali 2003). In this ...

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...sequence alignment, rather than borrowing Cartesian coordinates directly (Sali and Blundell 1993). Although improvements in identification (Karplus et al. 1998; Jones et al. 1999), alignment quality (=-=Sauder et al. 2000-=-) and side-chain prediction methods (Bower et al. 1997; Dunbrack Jr. 1999; Mendes et al. 2001; Xiang and Honig 2001; Liang and Grishin 2002) have been significant in recent years, loop modeling remain...

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... and silent delete states. The number of repeated elements is the length of the model. Each element of a match, insert and delete state models a position in the consensus sequence of the sequence family and describes sequence homology. Another commonly used approach is dynamic programming. Dynamic programming is a mathematically rigorous technique because it is guaranteed to find the optimal alignment (26). MSA is simply an extension of pairwise sequence alignment. MSA is the process of aligning three or more sequences simultaneously to bring as many similar residues into register as possible (4, 25). The resulting alignments are commonly interpreted in two contexts; (a) to find regions that define a conserved pattern or domain; and (b) to derive the possible phylogeny or evolutionary relationships among the sequences (12). The presence of similar domains across multiple sequences implies a similar biochemical function or higher-level structure that may be used as the basis for further experimental investigation. 2.1 Dynamic Programming DP is a commonly used recurrence method for solving sequential or multi-stage decision problems (11, 22). The essence of DP is the principle of optimality...