lecture13_S2009

lecture13_S2009 - 18.417:ProteinSecondaryStructure...

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    18.417: Protein Secondary Structure  Prediction Jerome Waldispuhl, Department of Mathematics, MIT Slides from Jinbo Xu (TTI, Chicago)
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    Secondary structure annotation
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    How to evaluate a prediction? correctly predicted residues         number of residues The Q 3   test:  = 3 Q Of course, all methods would be tested on  the same proteins.
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    AADGAAUAHHLAVVGTQYLLIMANPLLAMNSFYCQLILL ..HHHHHH. .TT. ..EEEETTEEEEEE. .HHHHHHH. .. ....HHHHHH. ...EEEEEE. ..EEEEEEEE. ..HHHHH Secondary structure annotation Sequence Observed structure Predicted structure
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    AADGAAUAHHLAVVGTQYLLIMANPLLAMNSFYCQLILL .. HH HHH H.. TT. . . EEEE TTEE EEEE .... . HH HH ... .. .. HHH HHH .... E EEEE E... EEEE EEEE . .. HH HHH Secondary structure annotation Helix:   observed:10, predicted:11, correct:5 Strand: observed:10, predicted:14, correct:8 NA:      observed:16, predicted:14, correct:7 Q3 = 0.56
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    • First  generation – single residue statistics         Fasman & Chou (1974) :       Some residues have particular secondary                        structure preference.         Examples: Glu                -Helix                                                  Val                 -strand β Old methods • Second generation – segment statistics Similar, but also considering adjacent residues.
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    Difficulties Bad accuracy - below 66% (Q3 results). Q3 of strands (E) : 28% - 48%. Predicted structures were too short.
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    Methods Accuracy Comparison
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    3 rd  generation methods • Third generation methods reached 77%  accuracy. • They consist of two new ideas:  1.  A biological idea  –       Using evolutionary information.  2.  A technological idea  –       Using neural networks.
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    Performance of secondary structure predictors across years
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    How can evolutionary information  help us? Homologues             similar structure  But sequences change up to 85%  Sequence would vary differently - depends on structure
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    How can evolutionary information  help us?  In defined secondary structures. In protein core’s segments (more hydrophobic). In amphipatic helices (cycle of hydrophobic  and hydrophilic residues).
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lecture13_S2009 - 18.417:ProteinSecondaryStructure...

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