tertiary structures. The approach to structure prediction based on mechanical models has the innate (possibly fatal) attraction that, in theory, it requires no prior knowledge of protein tertiary structure. If successful it could be applied uniformly to all sequences. By contrast, all methods based on inference from known structures are inherently limited in their applicability. They will only be appropriate for predicting structures similar to those, which were used in the inference process. Fortunately there are often biophysical or biochemical clues that help make this decision and these are often integrated in the methods for structure prediction. Currently the best way to achieve reasonable secondary structure predictions is to run a variety of prediction algorithms over your sequence and determine a consensus among the results. There are various web servers that will do these multiple analyses for you. As yet, coverage of secondary structure prediction within EMBOSS is limited. More algorithms will be added to enable the consensus approach described above. We'll take a look now at some of the predictions you can currently perform using EMBOSS. •pepinfo pepinfo •Exercise: transmembrane regions •Predicting tmap •Exercise: Pepinfo Pepinfo produces information on amino acid properties (size, polarity, aromaticity, charge etc). Hydrophobicity profiles are also available and are useful for locating turns, potential antigenic peptides and transmembrane helices. Various algorithms are employed including the Kyte and Doolittle hydropathy measure - this curve is the average of a residue-specific hydrophobicity index over a window of nine residues. When the line is in the upper half of the frame, it indicates a hydrophobic region, and when it is in the lower half, a hydrophilic region. Exercise: pepinfo Program: pepinfo choose xlrhodop.pep Remember that you produced this in a previous exercise. Plots simple amino acid properties in Graph type [png]: You will see pictures that look like this:
tertiary structures. The approach to structure prediction based on mechanical models has the innate (possibly fatal) attraction that, in theory, it requires no prior knowledge of protein tertiary structure. If successful it could be applied uniformly to all sequences. By contrast, all methods based on inference from known structures are inherently limited in their applicability. They will only be appropriate for predicting structures similar to those, which were used in the inference process. Fortunately there are often biophysical or biochemical clues that help make this decision and these are often integrated in the methods for structure prediction. Currently the best way to achieve reasonable secondary structure predictions is to run a variety of prediction algorithms over your sequence and determine a consensus among the results. There are various web servers that will do these multiple analyses for you. As yet, coverage of secondary structure prediction within EMBOSS is limited. More algorithms will be added to enable the consensus approach described above. We'll take a look now at some of the predictions you can currently perform using EMBOSS. •pepinfo •Exercise: pepinfo •Predicting transmembrane regions •Exercise: tmap Pepinfo Pepinfo produces information on amino acid properties (size, polarity, aromaticity, charge etc). Hydrophobicity profiles are also available and are useful for locating turns, potential antigenic peptides and transmembrane helices. Various algorithms are employed including the Kyte and Doolittle hydropathy measure - this curve is the average of a residue-specific hydrophobicity index over a window of nine residues. When the line is in the upper half of the frame, it indicates a hydrophobic region, and when it is in the lower half, a hydrophilic region. Exercise: pepinfo Program: pepinfo choose xlrhodop.pep Remember that you produced this in a previous exercise. Plots simple amino acid properties in Graph type [png]: You will see pictures that look like this:
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