A review of visualisations of protein fold networks and their relationship with sequence and function.

Proteins form arguably the most significant link between genotype and phenotype. Understanding the relationship between protein sequence and structure, and applying this knowledge to predict function, is difficult. One way to investigate these relationships is by considering the space of protein folds and how one might move from fold to fold through similarity, or potential evolutionary relationships.

Unattained geometric configurations of secondary structure elements in protein structural space.

Discovery of new folds in the Protein Data Bank (PDB) has all but ceased. This could be viewed as evidence that all existing protein folds have been documented. Sampling bias has, however, been presented as an alternative explanation.

Benchmarking Methods of Protein Structure Alignment.

The function of a protein is primarily determined by its structure and amino acid sequence. Many biological questions of interest rely on being able to accurately determine the group of structures to which domains of a protein belong; this can be done through alignment and comparison of protein structures. Dozens of different methods for Protein Structure Alignment (PSA) have been proposed that use a wide range of techniques.