Calculating the Secrets of Life Contributions of the Mathematical Sciences to Molecular Biology (1995) / Chapter Skim
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Pages 255-264
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From page 255... ...
when compared to the known aspartyl proteases (~ 240 amino acids) and that it contained only one of the two kev asnar~vl groups that form the active site Moreover the Clerk elf In similarity between the viral sequence and the known aspartyl proteases was sufficiently low that researchers were unsure of exactly what went I
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From page 256... ...
This suggests a computational strategy to relate protein sequence and structure. First, predict the location of a-helices and ,8-strands, and then pack secondary structure units together to form an approximate tertiary structure that can be refined to the folded protein structure (see Figure 9.71.
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Two general strategies have been applied to the secondary structure prediction problem: statistical approaches and rule-based approaches. The statistical approaches assert that proteins of known tertiary structure provide a useful data set describing secondary structure preferences of individual amino acids.
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Additional protein crystal structures and studies on model peptide systems wait help in overcoming these limitations. In 1974, a landmark paper on protein secondary structure prediction was published by Chou and Fasman (1974~.
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It is useful to explore the connection weights derived by the network that relate amino acids to their secondary structure preferences. Figure 9.10 is a Hinton diagram of these weights (the magnitude of the weight is proportional to the area of the square; positive weights are in white, and negative weights are in black)
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From page 260... ...
There are three output units: helix, strand, and coil. Each input unit is connected to each output unit, and the output unit with the greatest output is taken to be the secondary structure prediction for the central amino acid.
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This is consistent with the structure information derived from previous studies and reinforces the sensibility of this approach. Why do neural networks not perform more accurately?
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Other aspects of this problem continue to make this a fertile area for study. The second general approach to secondary structure prediction is rulebased methods, which try to capture biochemical regularities in protein structure.
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From page 264... ...
The hierarchical approach to protein structure prediction is premised on the notion that secondary structure wall be a users] computational intermediate for the prediction of overall tertiary structure.
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