A generalized analysis of hydrophobic and loop clusters within globular protein sequences.

ABSTRACT:

Background

Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet.

Results

The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated

SUBMITTER: Eudes R 

PROVIDER: S-EPMC1774571 | biostudies-literature | 2007 Jan

REPOSITORIES: biostudies-literature