Abstract
ProtoNet is an automatic hierarchical classification of the protein sequence space. In 2004, the ProtoNet (version 4.0) presents the analysis of over one million proteins merged from SwissProt and TrEMBL databases. In addition to rich visualization and analysis tools to navigate the clustering hierarchy, we incorporated several improvements that allow a simplified view of the scaffold of the proteins. An unsupervised, biologically valid method that was developed resulted in a condensation of the ProtoNet hierarchy to only 12% of the clusters. A large portion of these clusters was automatically assigned high confidence biological names according to their correspondence with functional annotations. ProtoNet is available at: http://www.protonet.cs.huji.ac.il.
| Original language | English |
|---|---|
| Pages (from-to) | D216-D218 |
| Journal | Nucleic Acids Research |
| Volume | 33 |
| Issue number | DATABASE ISS. |
| DOIs | |
| State | Published - 1 Jan 2005 |
Bibliographical note
Funding Information:We thank the entire current and previous ProtoNet teams for their endless support. Special thanks to Alex Savenok for the web design as well as for the development of the visualization tools. We thank the fellowship support by the Sudarsky Center for Computational Biology (SCCB) to N.K., U.I., M.F. and M.F.. This study is partially supported by the EU NoE BioSapiens consortium and the CESG consortium supported by the NIH.