Contents:

1 Introduction.
1.1 Structural Biology.

1.2 Overview of Protein Structure Prediction.

1.3 Protein Structure Prediction - Feasible Goals.

1.4 Basic Approaches to structure prediction.

1.5 Practical Protein Structure Prediction.

2 Protein Structure - What to predict?.

2.1 Introduction.

2.2 Primary Structure.

2.3 Secondary Structure.

2.4 Structural Domains and structural class.

2.5 Super Secondary Structure/Topological motifs.

2.6 Tertiary and Quaternary Structure.

2.7 Protein Structure Representation.

2.8 Evaluation of structures by statistical methods.

3 Comparison of sequence and structure.

3.1 Similarity is a fundamental concept.

3.2 Similarity of protein sequence, structure and function.

3.3 Describing similarity between proteins.

3.4 Measurement of similarity in protein structure.

3.5 Protein Structure Classification.

3.6 Similarity of protein sequence.

3.7 Statistical measures of similarity.

4 Sequence Alignment & Database Searching.

4.1 Finding the best score for the alignment of two
sequences.

4.2 Finding the best alignment of two sequences - dynamic
programming.

4.3 Variations on a theme.

4.4 Searching DNA databases with a protein sequence or
alignment.

4.5 Approximations for speed - BLAST and FASTA.

4.6 Dot plots - getting an overview of all similarities.

4.7 Alternative alignments for same sequences.

4.8 Analysis of groups of sequences.

4.9 Multiple Sequence Alignment.

4.10 Searching sequence databases with a multiple alignment or
'profile'.

4.11 Iterative database searching.

4.12 Databases of Alignments.

4.13 Assessing Accuracy of Alignment Methods.

5 Protein Structure Prediction by Similarity.

5.1 Protein fold recognition.

5.2 Homology Modelling.

6 Protein secondary structure prediction.

6.1 Prediction from single sequences.

6.2 Prediction from multiple alignment.

6.3 Automatic methods.

6.4 Accuracy of secondary structure prediction.

6.5 Prediction of buried residues.

6.6 Prediction of transmembrane protein structure.

6.7 Prediction of coiled coils.

6.8 Practical Application of Secondary structure prediction.

7 How Useful is structure prediction - perspectives for the
future.

7.1 Future of structure determination and prediction.

7.2 Large-Scale Prediction.

7.3 Structural Genomics - Large-Scale Structure
Determination.

7.4 Will the prediction problem go away?.

.

A Structure determination methods.

A.1 X-Ray crystallography.

A.2 Structure Determination by NMR.

B Storage of information on macromolecular structure.

B.1 Flat files.

B.2 Relational Databases.

B.3 Object Databases.

C Internet Resources for the Structure Predictor.

D References.

E Figures.

F Tables