Alignment target-based

Currently, methods of structure prediction from sequence perform poorly. The results of the biannual CASP experiment (Critical Assessment of techniques for protein Structure Prediction see http //predictioncenter.llnl. gov/) are equivocal to say the least. A recent report on the improvements of aligning target sequences to a structural template (67) indicates that over the last four CASP competitions there was no significant improvement in quality in this key step in the prediction process. Alignment remains the major source of error in all models based on less than 30% se-... 

Fig. 1. Position-specific scoring matrix model representation. The information contained in a set of aligned target sites (A) is initially encoded into a count matrix (B) in which each column represents the number of sequences that contain each of the four bases in that position. For practical purposes, the count matrix is further transformed into some form of log-frequency matrix (C). Any of the three forms of information can be graphically represented as a LOGO of symbols (D).

Fig. 4. Flowchart for target-based chromatographic alignment, adapted from (Johnson et al., 2003).

The molecular overlay experiment orients the molecules to hnd the best RMS or held ht. The held ht is based on electrostatic and steric interactions. The application can hnd either the best total alignment of all molecules or the best match of all molecules to a specihed target molecule. Alignment can include a database search for conformers that show the best alignment based on the molecules under study. 

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