Some gory details of protein secondary structure prediction

9/12/01


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Table of Contents

Some gory details of protein secondary structure prediction

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Goal of secondary structure prediction

Secondary structure predictions of 1. and 2. generation

Helix formation is local

b-sheet formation is NOT local

Problems of secondary structure predictions (before 1994)

Simple neural network

Training a neural network 1

Training a neural network 2

Training a neural network 3

Training a neural network 4

Neural networks classify points

Simple neural network with hidden layer

Neural Network for secondary structure

Secondary structure predictions of 1. and 2. generation

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Balanced training

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PHDsec: structure-to-structure network

Better prediction of segment lengths

Evolution has it!

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Spectrin homology domain (SH3)

Prediction accuracy varies!

Why so bad?

Stronger predictions more accurate!

Correct prediction of correctly predicted residues

BAD errors are frequent!

False prediction for engineered proteins!

PHDsec: the un-g(l)ory details

Details PHDsec: Multiple alignment

PHDsec: the un-g(l)ory details

Details PHDsec: Multiple alignment

Secondary structure prediction

Secondary structure prediction 2000

Prediction of protein secondary structure

CAFASP statistics

CAFASP sec unique

CAFASP sec homologous

CAFASP concept

What is significant

Rank only if significant

EVA: automatic continuous EVAluation of structure prediction

EVA: automatic continuous EVAluation of structure prediction

EVA: secondary structure

EVA: secondary structure

Accuracy varies for proteins!

Averaging over many methods not always a good idea!

Some proteins predicted better

Reliability correlates with accuracy!

Conclusion

Availability of methods

Author: Burkhard Rost

Email: rost@columbia.edu

Home Page: http://cubic.bioc.columbia.edu

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