Protein sequence-structure alignment errors

When predicting consensus structures, be aware that the quality of the prediction is limited by the quality of the input alignment. Nucleic acid alignments are generally more error-prone than protein alignments. For coding sequences it is sometimes preferable to back-translate a protein alignment. 

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-... 

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