Bioinformatics of Protein Function

The following sections are included:

• Introduction

• Evolution of Protein Sequence, Structure and Function

  • Natural Mechanisms of Development of Novel Protein Functions

    • Divergence

    • Recruitment

    • "Mixing and matching" of domains, including duplication/oligomerization, and domain swapping or fusion

• Definition and Classification of Protein Function

• Classification Schemes for Protein Function

  • General Schemes

  • The Enzyme Commission Classification

  • The Gene Ontology Consortium

  • Comparison of Enzyme Commission and GO Classifications

• Methods for Assigning Protein Function

  • Detection of Protein Homology from Sequence, and its Application to Function Assignment

  • Detection of Structural Similarity, and Structure/Function Correlations

  • Prediction of Ligands

  • Motifs as Functional Signatures

  • Databases of single motifs

  • Function Identification from Sequence by Feature Extraction

• Applications of Full-Organism Information: Inferences from Genomic Context and Protein Interaction Patterns

  • Inference of Function from Metabolic Pathways

• Microarrays

  • Chromatin Immunoprecipitation

• Conclusions

• References