ProTarget: automatic prediction of protein structure novelty | Zendy

Ori Sasson | Zendy; Michal Linial | Zendy

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ProTarget: automatic prediction of protein structure novelty

Author(s) -

Ori Sasson,

Michal Linial

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki389

Subject(s) - structural classification of proteins database , protein data bank (rcsb pdb) , structural genomics , biology , cluster analysis , protein data bank , sequence (biology) , protein sequencing , sequence alignment , protein structure prediction , similarity (geometry) , protein structure database , computational biology , protein methods , novelty , protein structure , visualization , bioinformatics , sequence analysis , peptide sequence , sequence database , computer science , data mining , genetics , artificial intelligence , gene , biochemistry , philosophy , theology , image (mathematics)

ProTarget is a Web-based tool for the automatic prediction of fold novelty. It offers the structural genomics community a method for target selection by providing an online analysis of any new or pre-existing sequence for its relationship to any previously solved three-dimensional structure. ProTarget takes as input an amino acid sequence. Regions of this sequence that exhibit high similarity to an existing PDB (Protein Data Bank) sequence are removed, leaving one or more subsequences. Each of these subsequences is then analyzed against a clustering of the protein space to determine the likelihood of its representing a new structural superfamily. This likelihood is derived from the distance in the clustering between the (sub)sequence and sequences that have known structures. The output of ProTarget is a graphical visualization of the protein of interest together with the likelihood that a protein sequence represents a novel structural superfamily. ProTarget is updated regularly and currently covers over 160 000 protein sequences from the SwissProt and PDB databases. ProTarget is available at http://www.protarget.cs.huji.ac.il.

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