Table of Contents for:Fold recognition by prediction-based threading

Burkhard Rost

1. Abstract
2. Introduction
3. Methods
   1. Brief outline of the algorithm
   2. Prediction of 1D structure
   3. Alignment of 1D structure
   4. Free parameters for dynamic programming
   5. Evaluation of prediction accuracy
   6. Data sets used for validation
   1. Results
      1. Fold recognition
      2. Remote homology modelling
      3. Comparison to other threading methods
   2. Conclusion
   3. Acknowledgements
   4. References
   5. Tables
      1. Table 1 Accuracy of fold detection
      2. Table 3 Detailed results for 89 test proteins
      3. Table 4 Performance on a favourable set of 11 proteins used by Jones et al., 1992
      4. Table 5 Performance on a set of 11 proteins used by Russell et al., 1996
      5. Table 6 Performance on the Asilomar 1994 threading targets
   6. Figures
      1. Fig. 1 Threading predicted 1D structure profiles into known 3D structures (method)
      2. Fig. 2 Empirical basis for 1D-3D threading
      3. Fig. 3 Similarity matrix for aligning 1D structure
      4. Fig. 4 Cumulative accuracy of detiction vs. rank of hit
      5. Fig. 5 Focusing on stronger predictions
      6. Fig. 6 Restricting test set to entire folds
      7. Fig. 7 Alignments for three correctly detected remote homologues
      8. Fig. 8 Structural and predicted alignments for heat-shock p70 and actin

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