ProtoNet: hierarchical classification of the protein space

Nucleic Acids Res. 2003 Jan 1;31(1):348-52. doi: 10.1093/nar/gkg096.


The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outcome of this clustering process is a classification of the input proteins into a hierarchy of clusters of varying degrees of granularity. ProtoNet (version 1.3) is accessible in the form of an interactive web site at ProtoNet provides navigation tools for monitoring the clustering process with a vertical and horizontal view. Each cluster at any level of the hierarchy is assigned with a statistical index, indicating the level of purity based on biological keywords such as those provided by SWISS-PROT and InterPro. ProtoNet can be used for function prediction, for defining superfamilies and subfamilies and for large-scale protein annotation purposes.

MeSH terms

  • Animals
  • Cluster Analysis
  • Databases, Protein*
  • Information Storage and Retrieval
  • Internet
  • Proteins / chemistry
  • Proteins / classification*
  • Proteins / physiology


  • Proteins